writer.R

#' Write code for loading libraries
#'
#' @param lib vector of libraries
#'
#' @rdname wrLib
#' @export wrLib
#'
wrLib <- function(lib) {
  oup = ""
  for(iLib in lib){
    oup = paste0(oup, "library(", iLib, ") \n")
  }
  glue::glue(paste0(oup, "\n"))
}

#' Write code for loading objects for server.R
#'
#' @param prefix file prefix 
#'
#' @rdname wrSVload
#' @export wrSVload
#'
wrSVload <- function(prefix) {
  glue::glue('{prefix}conf = readRDS("{prefix}conf.rds")\n',
             '{prefix}def  = readRDS("{prefix}def.rds")\n',
             '{prefix}gene = readRDS("{prefix}gene.rds")\n',
             '{prefix}meta = readRDS("{prefix}meta.rds")\n',
             '\n\n\n\n')
}

#' Write code for fixed portion of server.R
#'
#' @rdname wrSVfix
#' @export wrSVfix
#'
wrSVfix <- function() {
  glue::glue('### Useful stuff \n',
             '# Colour palette \n',
             'cList = list(c("grey85","#FFF7EC","#FEE8C8","#FDD49E","#FDBB84", \n',
             '               "#FC8D59","#EF6548","#D7301F","#B30000","#7F0000"), \n',
             '             c("#4575B4","#74ADD1","#ABD9E9","#E0F3F8","#FFFFBF", \n',
             '               "#FEE090","#FDAE61","#F46D43","#D73027")[c(1,1:9,9)], \n',
             '             c("#FDE725","#AADC32","#5DC863","#27AD81","#21908C", \n',
             '               "#2C728E","#3B528B","#472D7B","#440154")) \n',
             'names(cList) = c("White-Red", "Blue-Yellow-Red", "Yellow-Green-Purple") \n',
             ' \n',
             '# Panel sizes \n',
             'pList = c("400px", "600px", "800px") \n',
             'names(pList) = c("Small", "Medium", "Large") \n',
             'pList2 = c("500px", "700px", "900px") \n',
             'names(pList2) = c("Small", "Medium", "Large") \n',
             'pList3 = c("600px", "800px", "1000px") \n',
             'names(pList3) = c("Small", "Medium", "Large") \n',
             'sList = c(18,24,30) \n',
             'names(sList) = c("Small", "Medium", "Large") \n',
             'lList = c(5,6,7) \n',
             'names(lList) = c("Small", "Medium", "Large") \n',
             ' \n',
             '# Function to extract legend \n',
             'g_legend <- function(a.gplot){{  \n',
             '  tmp <- ggplot_gtable(ggplot_build(a.gplot))  \n',
             '  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")  \n',
             '  legend <- tmp$grobs[[leg]]  \n',
             '  legend \n',
             '}}  \n',
             ' \n',
             '# Plot theme \n',
             'sctheme <- function(base_size = 24, XYval = TRUE, Xang = 0, XjusH = 0.5){{ \n',
             '  oupTheme = theme( \n',
             '    text =             element_text(size = base_size, family = "Helvetica"), \n',
             '    panel.background = element_rect(fill = "white", colour = NA), \n',
             '    axis.line =   element_line(colour = "black"), \n',
             '    axis.ticks =  element_line(colour = "black", size = base_size / 20), \n',
             '    axis.title =  element_text(face = "bold"), \n',
             '    axis.text =   element_text(size = base_size), \n',
             '    axis.text.x = element_text(angle = Xang, hjust = XjusH), \n',
             '    legend.position = "bottom", \n',
             '    legend.key =      element_rect(colour = NA, fill = NA) \n',
             '  ) \n',
             '  if(!XYval){{ \n',
             '    oupTheme = oupTheme + theme( \n',
             '      axis.text.x = element_blank(), axis.ticks.x = element_blank(), \n',
             '      axis.text.y = element_blank(), axis.ticks.y = element_blank()) \n',
             '  }} \n',
             '  return(oupTheme) \n',
             '}} \n',
             ' \n',
             '### Common plotting functions \n',
             '# Plot cell information on dimred \n',
             'scDRcell <- function(inpConf, inpMeta, inpdrX, inpdrY, inp1, inpsub1, inpsub2, \n',
             '                     inpsiz, inpcol, inpord, inpfsz, inpasp, inptxt, inplab){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inpdrX]$ID, inpConf[UI == inpdrY]$ID, \n',
             '                       inpConf[UI == inp1]$ID, inpConf[UI == inpsub1]$ID),  \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("X", "Y", "val", "sub") \n',
             '  rat = (max(ggData$X) - min(ggData$X)) / (max(ggData$Y) - min(ggData$Y)) \n',
             '  bgCells = FALSE \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    bgCells = TRUE \n',
             '    ggData2 = ggData[!sub %in% inpsub2] \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  if(inpord == "Max-1st"){{ \n',
             '    ggData = ggData[order(val)] \n',
             '  }} else if(inpord == "Min-1st"){{ \n',
             '    ggData = ggData[order(-val)] \n',
             '  }} else if(inpord == "Random"){{ \n',
             '    ggData = ggData[sample(nrow(ggData))] \n',
             '  }} \n',
             '  \n',
             '  # Do factoring if required \n',
             '  if(!is.na(inpConf[UI == inp1]$fCL)){{ \n',
             '    ggCol = strsplit(inpConf[UI == inp1]$fCL, "\\\\|")[[1]] \n',
             '    names(ggCol) = levels(ggData$val) \n',
             '    ggLvl = levels(ggData$val)[levels(ggData$val) %in% unique(ggData$val)] \n',
             '    ggData$val = factor(ggData$val, levels = ggLvl) \n',
             '    ggCol = ggCol[ggLvl] \n',
             '  }} \n',
             ' \n',
             '  # Actual ggplot \n',
             '  ggOut = ggplot(ggData, aes(X, Y, color = val)) \n',
             '  if(bgCells){{ \n',
             '    ggOut = ggOut + \n',
             '      geom_point(data = ggData2, color = "snow2", size = inpsiz, shape = 16) \n',
             '  }} \n',
             '  ggOut = ggOut + \n',
             '    geom_point(size = inpsiz, shape = 16) + xlab(inpdrX) + ylab(inpdrY) + \n',
             '    sctheme(base_size = sList[inpfsz], XYval = inptxt) \n',
             '  if(is.na(inpConf[UI == inp1]$fCL)){{ \n',
             '    ggOut = ggOut + scale_color_gradientn("", colours = cList[[inpcol]]) + \n',
             '      guides(color = guide_colorbar(barwidth = 15)) \n',
             '  }} else {{ \n',
             '    sListX = min(nchar(paste0(levels(ggData$val), collapse = "")), 200) \n',
             '    sListX = 0.75 * (sList - (1.5 * floor(sListX/50))) \n',
             '    ggOut = ggOut + scale_color_manual("", values = ggCol) + \n',
             '      guides(color = guide_legend(override.aes = list(size = 5),  \n',
             '                                  nrow = inpConf[UI == inp1]$fRow)) + \n',
             '      theme(legend.text = element_text(size = sListX[inpfsz])) \n',
             '    if(inplab){{ \n',
             '      ggData3 = ggData[, .(X = mean(X), Y = mean(Y)), by = "val"] \n',
             '      lListX = min(nchar(paste0(ggData3$val, collapse = "")), 200) \n',
             '      lListX = lList - (0.25 * floor(lListX/50)) \n',
             '      ggOut = ggOut + \n',
             '        geom_text_repel(data = ggData3, aes(X, Y, label = val), \n',
             '                        color = "grey10", bg.color = "grey95", bg.r = 0.15, \n',
             '                        size = lListX[inpfsz], seed = 42) \n',
             '    }} \n',
             '  }} \n',
             '  if(inpasp == "Square") {{ \n',
             '    ggOut = ggOut + coord_fixed(ratio = rat) \n',
             '  }} else if(inpasp == "Fixed") {{ \n',
             '    ggOut = ggOut + coord_fixed() \n',
             '  }} \n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             'scDRnum <- function(inpConf, inpMeta, inp1, inp2, inpsub1, inpsub2, \n',
             '                    inpH5, inpGene, inpsplt){{ \n', 
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inp1]$ID, inpConf[UI == inpsub1]$ID), \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("group", "sub") \n',
             '  h5file <- H5File$new(inpH5, mode = "r") \n',
             '  h5data <- h5file[["grp"]][["data"]] \n',
             '  ggData$val2 = h5data$read(args = list(inpGene[inp2], quote(expr=))) \n',
             '  ggData[val2 < 0]$val2 = 0 \n',
             '  h5file$close_all() \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n', 
             '  \n',
             '  # Split inp1 if necessary \n',
             '  if(is.na(inpConf[UI == inp1]$fCL)){{ \n',
             '    if(inpsplt == "Quartile"){{nBk = 4}} \n', 
             '    if(inpsplt == "Decile"){{nBk = 10}} \n', 
             '    ggData$group = cut(ggData$group, breaks = nBk) \n',
             '  }} \n',
             '  \n',
             '  # Actual data.table \n',
             '  ggData$express = FALSE \n',
             '  ggData[val2 > 0]$express = TRUE \n',
             '  ggData1 = ggData[express == TRUE, .(nExpress = .N), by = "group"] \n',
             '  ggData = ggData[, .(nCells = .N), by = "group"] \n',
             '  ggData = ggData1[ggData, on = "group"] \n',
             '  ggData = ggData[, c("group", "nCells", "nExpress"), with = FALSE] \n',
             '  ggData[is.na(nExpress)]$nExpress = 0 \n',
             '  ggData$pctExpress = 100 * ggData$nExpress / ggData$nCells \n',
             '  ggData = ggData[order(group)] \n',
             '  colnames(ggData)[3] = paste0(colnames(ggData)[3], "_", inp2) \n',
             '  return(ggData) \n',
             '}} \n',
             '# Plot gene expression on dimred \n',
             'scDRgene <- function(inpConf, inpMeta, inpdrX, inpdrY, inp1, inpsub1, inpsub2, \n',
             '                     inpH5, inpGene, \n',
             '                     inpsiz, inpcol, inpord, inpfsz, inpasp, inptxt){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inpdrX]$ID, inpConf[UI == inpdrY]$ID, \n',
             '                       inpConf[UI == inpsub1]$ID),  \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("X", "Y", "sub") \n',
             '  rat = (max(ggData$X) - min(ggData$X)) / (max(ggData$Y) - min(ggData$Y)) \n',
             '  \n',
             '  h5file <- H5File$new(inpH5, mode = "r") \n',
             '  h5data <- h5file[["grp"]][["data"]] \n',
             '  ggData$val = h5data$read(args = list(inpGene[inp1], quote(expr=))) \n',
             '  ggData[val < 0]$val = 0 \n',
             '  h5file$close_all() \n',
             '  bgCells = FALSE \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    bgCells = TRUE \n',
             '    ggData2 = ggData[!sub %in% inpsub2] \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  if(inpord == "Max-1st"){{ \n',
             '    ggData = ggData[order(val)] \n',
             '  }} else if(inpord == "Min-1st"){{ \n',
             '    ggData = ggData[order(-val)] \n',
             '  }} else if(inpord == "Random"){{ \n',
             '    ggData = ggData[sample(nrow(ggData))] \n',
             '  }} \n',
             '   \n',
             '  # Actual ggplot \n',
             '  ggOut = ggplot(ggData, aes(X, Y, color = val)) \n',
             '  if(bgCells){{ \n',
             '    ggOut = ggOut + \n',
             '      geom_point(data = ggData2, color = "snow2", size = inpsiz, shape = 16) \n',
             '  }} \n',
             '  ggOut = ggOut + \n',
             '    geom_point(size = inpsiz, shape = 16) + xlab(inpdrX) + ylab(inpdrY) + \n',
             '    sctheme(base_size = sList[inpfsz], XYval = inptxt) +  \n',
             '    scale_color_gradientn(inp1, colours = cList[[inpcol]]) + \n',
             '      guides(color = guide_colorbar(barwidth = 15)) \n',
             '  if(inpasp == "Square") {{ \n',
             '    ggOut = ggOut + coord_fixed(ratio = rat) \n',
             '  }} else if(inpasp == "Fixed") {{ \n',
             '    ggOut = ggOut + coord_fixed() \n',
             '  }} \n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             '# Plot gene coexpression on dimred \n',
             'bilinear <- function(x,y,xy,Q11,Q21,Q12,Q22){{ \n',
             '  oup = (xy-x)*(xy-y)*Q11 + x*(xy-y)*Q21 + (xy-x)*y*Q12 + x*y*Q22 \n',
             '  oup = oup / (xy*xy) \n',
             '  return(oup) \n',
             '}} \n',
             'scDRcoex <- function(inpConf, inpMeta, inpdrX, inpdrY, inp1, inp2, \n',
             '                     inpsub1, inpsub2, inpH5, inpGene, \n',
             '                     inpsiz, inpcol, inpord, inpfsz, inpasp, inptxt){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inpdrX]$ID, inpConf[UI == inpdrY]$ID, \n',
             '                       inpConf[UI == inpsub1]$ID),  \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("X", "Y", "sub") \n',
             '  rat = (max(ggData$X) - min(ggData$X)) / (max(ggData$Y) - min(ggData$Y)) \n',
             '  \n',
             '  h5file <- H5File$new(inpH5, mode = "r") \n',
             '  h5data <- h5file[["grp"]][["data"]] \n',
             '  ggData$val1 = h5data$read(args = list(inpGene[inp1], quote(expr=))) \n',
             '  ggData[val1 < 0]$val1 = 0 \n',
             '  ggData$val2 = h5data$read(args = list(inpGene[inp2], quote(expr=))) \n',
             '  ggData[val2 < 0]$val2 = 0 \n',
             '  h5file$close_all() \n',
             '  bgCells = FALSE \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    bgCells = TRUE \n',
             '    ggData2 = ggData[!sub %in% inpsub2] \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  \n',
             '  # Generate coex color palette \n',
             '  cInp = strsplit(inpcol, "; ")[[1]] \n',
             '  if(cInp[1] == "Red (Gene1)"){{ \n',
             '    c10 = c(255,0,0) \n',
             '  }} else if(cInp[1] == "Orange (Gene1)"){{ \n',
             '    c10 = c(255,140,0) \n',
             '  }} else {{ \n',
             '    c10 = c(0,255,0) \n',
             '  }} \n',
             '  if(cInp[2] == "Green (Gene2)"){{ \n',
             '    c01 = c(0,255,0) \n',
             '  }} else {{ \n',
             '    c01 = c(0,0,255) \n',
             '  }} \n',
             '  c00 = c(217,217,217) ; c11 = c10 + c01 \n',
             '  nGrid = 16; nPad = 2; nTot = nGrid + nPad * 2 \n',
             '  gg = data.table(v1 = rep(0:nTot,nTot+1), v2 = sort(rep(0:nTot,nTot+1))) \n',
             '  gg$vv1 = gg$v1 - nPad ; gg[vv1 < 0]$vv1 = 0; gg[vv1 > nGrid]$vv1 = nGrid \n',
             '  gg$vv2 = gg$v2 - nPad ; gg[vv2 < 0]$vv2 = 0; gg[vv2 > nGrid]$vv2 = nGrid \n',
             '  gg$cR = bilinear(gg$vv1, gg$vv2, nGrid, c00[1], c10[1], c01[1], c11[1]) \n',
             '  gg$cG = bilinear(gg$vv1, gg$vv2, nGrid, c00[2], c10[2], c01[2], c11[2]) \n',
             '  gg$cB = bilinear(gg$vv1, gg$vv2, nGrid, c00[3], c10[3], c01[3], c11[3]) \n',
             '  gg$cMix = rgb(gg$cR, gg$cG, gg$cB, maxColorValue = 255) \n',
             '  gg = gg[, c("v1", "v2", "cMix")] \n',
             '  \n',
             '  # Map colours \n',
             '  ggData$v1 = round(nTot * ggData$val1 / max(ggData$val1)) \n',
             '  ggData$v2 = round(nTot * ggData$val2 / max(ggData$val2)) \n',
             '  ggData$v0 = ggData$v1 + ggData$v2 \n',
             '  ggData = gg[ggData, on = c("v1", "v2")] \n',
             '  if(inpord == "Max-1st"){{ \n',
             '    ggData = ggData[order(v0)] \n',
             '  }} else if(inpord == "Min-1st"){{ \n',
             '    ggData = ggData[order(-v0)] \n',
             '  }} else if(inpord == "Random"){{ \n',
             '    ggData = ggData[sample(nrow(ggData))] \n',
             '  }} \n',
             '  \n',
             '  # Actual ggplot \n',
             '  ggOut = ggplot(ggData, aes(X, Y)) \n',
             '  if(bgCells){{ \n',
             '    ggOut = ggOut + \n',
             '      geom_point(data = ggData2, color = "snow2", size = inpsiz, shape = 16) \n',
             '  }} \n',
             '  ggOut = ggOut + \n',
             '    geom_point(size = inpsiz, shape = 16, color = ggData$cMix) + \n',
             '    xlab(inpdrX) + ylab(inpdrY) + \n',
             '    sctheme(base_size = sList[inpfsz], XYval = inptxt) + \n',
             '    scale_color_gradientn(inp1, colours = cList[[1]]) + \n',
             '    guides(color = guide_colorbar(barwidth = 15)) \n',
             '  if(inpasp == "Square") {{ \n',
             '    ggOut = ggOut + coord_fixed(ratio = rat) \n',
             '  }} else if(inpasp == "Fixed") {{ \n',
             '    ggOut = ggOut + coord_fixed() \n',
             '  }} \n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             'scDRcoexLeg <- function(inp1, inp2, inpcol, inpfsz){{ \n',
             '  # Generate coex color palette \n',
             '  cInp = strsplit(inpcol, "; ")[[1]] \n',
             '  if(cInp[1] == "Red (Gene1)"){{ \n',
             '    c10 = c(255,0,0) \n',
             '  }} else if(cInp[1] == "Orange (Gene1)"){{ \n',
             '    c10 = c(255,140,0) \n',
             '  }} else {{ \n',
             '    c10 = c(0,255,0) \n',
             '  }} \n',
             '  if(cInp[2] == "Green (Gene2)"){{ \n',
             '    c01 = c(0,255,0) \n',
             '  }} else {{ \n',
             '    c01 = c(0,0,255) \n',
             '  }} \n',
             '  c00 = c(217,217,217) ; c11 = c10 + c01 \n',
             '  nGrid = 16; nPad = 2; nTot = nGrid + nPad * 2 \n',
             '  gg = data.table(v1 = rep(0:nTot,nTot+1), v2 = sort(rep(0:nTot,nTot+1))) \n',
             '  gg$vv1 = gg$v1 - nPad ; gg[vv1 < 0]$vv1 = 0; gg[vv1 > nGrid]$vv1 = nGrid \n',
             '  gg$vv2 = gg$v2 - nPad ; gg[vv2 < 0]$vv2 = 0; gg[vv2 > nGrid]$vv2 = nGrid \n',
             '  gg$cR = bilinear(gg$vv1, gg$vv2, nGrid, c00[1], c10[1], c01[1], c11[1]) \n',
             '  gg$cG = bilinear(gg$vv1, gg$vv2, nGrid, c00[2], c10[2], c01[2], c11[2]) \n',
             '  gg$cB = bilinear(gg$vv1, gg$vv2, nGrid, c00[3], c10[3], c01[3], c11[3]) \n',
             '  gg$cMix = rgb(gg$cR, gg$cG, gg$cB, maxColorValue = 255) \n',
             '  gg = gg[, c("v1", "v2", "cMix")] \n',
             '  \n',
             '  # Actual ggplot \n',
             '  ggOut = ggplot(gg, aes(v1, v2)) + \n',
             '    geom_tile(fill = gg$cMix) + \n',
             '    xlab(inp1) + ylab(inp2) + coord_fixed(ratio = 1) + \n',
             '    scale_x_continuous(breaks = c(0, nTot), label = c("low", "high")) + \n',
             '    scale_y_continuous(breaks = c(0, nTot), label = c("low", "high")) + \n',
             '    sctheme(base_size = sList[inpfsz], XYval = TRUE) \n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             'scDRcoexNum <- function(inpConf, inpMeta, inp1, inp2, \n',
             '                        inpsub1, inpsub2, inpH5, inpGene){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inpsub1]$ID), with = FALSE] \n',
             '  colnames(ggData) = c("sub") \n',
             '  h5file <- H5File$new(inpH5, mode = "r") \n',
             '  h5data <- h5file[["grp"]][["data"]] \n',
             '  ggData$val1 = h5data$read(args = list(inpGene[inp1], quote(expr=))) \n',
             '  ggData[val1 < 0]$val1 = 0 \n',
             '  ggData$val2 = h5data$read(args = list(inpGene[inp2], quote(expr=))) \n',
             '  ggData[val2 < 0]$val2 = 0 \n',
             '  h5file$close_all() \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  \n',
             '  # Actual data.table \n',
             '  ggData$express = "none" \n',
             '  ggData[val1 > 0]$express = inp1 \n',
             '  ggData[val2 > 0]$express = inp2 \n',
             '  ggData[val1 > 0 & val2 > 0]$express = "both" \n',
             '  ggData$express = factor(ggData$express, levels = unique(c("both", inp1, inp2, "none"))) \n',
             '  ggData = ggData[, .(nCells = .N), by = "express"] \n',
             '  ggData$percent = 100 * ggData$nCells / sum(ggData$nCells) \n',
             '  ggData = ggData[order(express)] \n',
             '  colnames(ggData)[1] = "expression > 0" \n',
             '  return(ggData) \n',
             '}} \n',
             ' \n',
             '# Plot violin / boxplot \n',
             'scVioBox <- function(inpConf, inpMeta, inp1, inp2, \n',
             '                     inpsub1, inpsub2, inpH5, inpGene, \n',     
             '                     inptyp, inppts, inpsiz, inpfsz){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inp1]$ID, inpConf[UI == inpsub1]$ID), \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("X", "sub") \n',
             '  \n',
             '  # Load in either cell meta or gene expr\n',
             '  if(inp2 %in% inpConf$UI){{ \n',
             '    ggData$val = inpMeta[[inpConf[UI == inp2]$ID]] \n',
             '  }} else {{ \n',
             '    h5file <- H5File$new(inpH5, mode = "r") \n',
             '    h5data <- h5file[["grp"]][["data"]] \n',
             '    ggData$val = h5data$read(args = list(inpGene[inp2], quote(expr=))) \n',
             '    ggData[val < 0]$val = 0 \n',
             '    set.seed(42) \n',
             '    tmpNoise = rnorm(length(ggData$val)) * diff(range(ggData$val)) / 1000 \n',
             '    ggData$val = ggData$val + tmpNoise \n',
             '    h5file$close_all() \n',
             '  }} \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  \n',
             '  # Do factoring \n',
             '  ggCol = strsplit(inpConf[UI == inp1]$fCL, "\\\\|")[[1]] \n',
             '  names(ggCol) = levels(ggData$X) \n',
             '  ggLvl = levels(ggData$X)[levels(ggData$X) %in% unique(ggData$X)] \n',
             '  ggData$X = factor(ggData$X, levels = ggLvl) \n',
             '  ggCol = ggCol[ggLvl] \n',
             '  \n',
             '  # Actual ggplot \n',
             '  if(inptyp == "violin"){{ \n',
             '    ggOut = ggplot(ggData, aes(X, val, fill = X)) + geom_violin(scale = "width") \n',
             '  }} else {{ \n',
             '    ggOut = ggplot(ggData, aes(X, val, fill = X)) + geom_boxplot() \n',
             '  }} \n',
             '  if(inppts){{ \n',
             '    ggOut = ggOut + geom_jitter(size = inpsiz, shape = 16) \n',
             '  }} \n',
             '  ggOut = ggOut + xlab(inp1) + ylab(inp2) + \n',
             '    sctheme(base_size = sList[inpfsz], Xang = 45, XjusH = 1) +  \n',
             '    scale_fill_manual("", values = ggCol) +\n',
             '    theme(legend.position = "none")\n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             '# Plot proportion plot \n',
             'scProp <- function(inpConf, inpMeta, inp1, inp2, inpsub1, inpsub2, \n',
             '                   inptyp, inpflp, inpfsz){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}} \n',
             '  # Prepare ggData \n',
             '  ggData = inpMeta[, c(inpConf[UI == inp1]$ID, inpConf[UI == inp2]$ID, \n',
             '                       inpConf[UI == inpsub1]$ID),  \n',
             '                   with = FALSE] \n',
             '  colnames(ggData) = c("X", "grp", "sub") \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
             '    ggData = ggData[sub %in% inpsub2] \n',
             '  }} \n',
             '  ggData = ggData[, .(nCells = .N), by = c("X", "grp")] \n',
             '  ggData = ggData[, {{tot = sum(nCells) \n',
             '                      .SD[,.(pctCells = 100 * sum(nCells) / tot, \n',
             '                             nCells = nCells), by = "grp"]}}, by = "X"] \n',
             '  \n',
             '  # Do factoring \n',
             '  ggCol = strsplit(inpConf[UI == inp2]$fCL, "\\\\|")[[1]] \n',
             '  names(ggCol) = levels(ggData$grp) \n',
             '  ggLvl = levels(ggData$grp)[levels(ggData$grp) %in% unique(ggData$grp)] \n',
             '  ggData$grp = factor(ggData$grp, levels = ggLvl) \n',
             '  ggCol = ggCol[ggLvl] \n',
             '  \n',
             '  # Actual ggplot \n',
             '  if(inptyp == "Proportion"){{ \n',
             '    ggOut = ggplot(ggData, aes(X, pctCells, fill = grp)) + \n',
             '      geom_col() + ylab("Cell Proportion (%)") \n',
             '  }} else {{ \n',
             '    ggOut = ggplot(ggData, aes(X, nCells, fill = grp)) + \n',
             '      geom_col() + ylab("Number of Cells") \n',
             '  }} \n',
             '  if(inpflp){{ \n',
             '    ggOut = ggOut + coord_flip() \n',
             '  }} \n',
             '  ggOut = ggOut + xlab(inp1) + \n',
             '    sctheme(base_size = sList[inpfsz], Xang = 45, XjusH = 1) +  \n',
             '    scale_fill_manual("", values = ggCol) + \n',
             '    theme(legend.position = "right") \n',
             '  return(ggOut) \n',
             '}} \n',
             ' \n',
             '# Get gene list \n',
             'scGeneList <- function(inp, inpGene){{ \n',
             '  geneList = data.table(gene = unique(trimws(strsplit(inp, ",|;|\n")[[1]])), \n',
             '                        present = TRUE) \n',
             '  geneList[!gene %in% names(inpGene)]$present = FALSE \n',
             '  return(geneList) \n',
             '}} \n',
             ' \n',
             '# Plot gene expression bubbleplot / heatmap \n',
             # Plot gene expression bubbleplot / heatmap 
			' scBubbHeat <- function(inpConf, inpMeta, inp, inpGrp, inpPlt, \n',
			'						inpsub1, inpsub2, inpH5, inpGene, inpScl, inpRow, inpCol, \n',
            '						inpcols, inpfsz, save = FALSE, splitBy = NULL){{   # Dave added splitBy parameter\n',
 			'  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}}\n', 
 			'  # Identify genes that are in our dataset \n',
 			'  geneList = scGeneList(inp, inpGene) \n',
 			'  geneList = geneList[present == TRUE] \n',
			'   shiny::validate(need(nrow(geneList) <= 50, "More than 50 genes to plot! Please reduce the gene list!")) \n',
			'   if (length(splitBy) == 0)  # Dave :: If there is not splitBy group defined check minimum number of genes\n',
			'   {{ shiny::validate(need(nrow(geneList) > 1, "Please input at least 2 genes to plot!"))  }}\n',
			'   else\n',
			'   {{  shiny::validate(need(inpGrp != splitBy, "Group and split cannot be the same !"))  }}\n\n',
 
   
 			'  # Prepare ggData \n\n',
  
			'   h5file <- H5File$new(inpH5, mode = "r") \n',
			'   h5data <- h5file[["grp"]][["data"]] \n',
			'   ggData = data.table() \n',
			'   for(iGene in geneList$gene){{ \n',
			'     tmp = inpMeta[, c("sampleID", inpConf[UI == inpsub1]$ID), with = FALSE] \n',
			'     colnames(tmp) = c("sampleID", "sub") \n',
			'     tmp$grpBy = inpMeta[[inpConf[UI == inpGrp]$ID]] \n', ##?this is absent in output
			' 	if (length(splitBy) != 0)								# Dave\n',
			' 	{{ tmp$splitBy = inpMeta[[inpConf[UI == splitBy]$ID]] }} # Dave \n',
			'     tmp$geneName = iGene \n',
			'     tmp$val = h5data$read(args = list(inpGene[iGene], quote(expr=))) \n',
			'     ggData = rbindlist(list(ggData, tmp)) \n',
			'   }} \n',
			'   h5file$close_all() \n',
			'   if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{ \n',
			'     ggData = ggData[sub %in% inpsub2] \n',
			'   }} \n',
			'   shiny::validate(need(uniqueN(ggData$grpBy) > 1, "Only 1 group present, unable to plot!")) \n',
			'   if (length(splitBy) != 0)\n',
			'   {{  shiny::validate(need(uniqueN(ggData$splitBy) > 1, "Only 1 splitBy group present, unable to plot!")) }}\n',

			'   # Aggregate \n',
			'   ggData$val = expm1(ggData$val)\n',
			'   selectedCols <- if (length(splitBy) == 0) c("geneName", "grpBy")  else c("geneName", "grpBy", "splitBy") # Dave\n',
			'   ggData = ggData[, .(val = mean(val), prop = sum(val>0) / length(sampleID)), \n',
			'                     by = selectedCols]   # Dave\n',
			' #                  by = c("geneName", "grpBy")] \n',
			'   ggData$val = log1p(ggData$val) \n',
			   
  			' # Scale if required \n',
  			' colRange = range(ggData$val) \n',
			'   if(inpScl == "Z-score"){{ \n',
			'     ggData[, val:= scale(val), keyby = "geneName"] \n',
			'     colRange = c(-max(abs(range(ggData$val))), max(abs(range(ggData$val)))) \n',
			'   }} \n',
			'  if(inpScl == "Fold change"){{ \n',
			'     ggData[, val:= scale(val,T,F), keyby = "geneName"] \n',
			'     colRange = c(-max(abs(range(ggData$val))), max(abs(range(ggData$val)))) \n',
			'   }} \n',
			'   # hclust row/col if necessary \n',
			'   ggMat = dcast.data.table(ggData, geneName~grpBy, value.var = "val") \n',
			'   tmp = ggMat$geneName \n',
			'   if (length(splitBy) != 0)  # Dave\n',
			'   {{ ggMat = dcast.data.table(ggData, splitBy~grpBy, value.var = "val") # Dave\n',
			'     tmp = ggMat$splitBy # Dave\n',
			'   }}\n',
			'   ggMat = as.matrix(ggMat[, -1]) \n',
			'   rownames(ggMat) = tmp \n',
			'	ggMat[is.na(ggMat)] <- 0 #Paul Added \n',
			'   if(inpRow){{ \n',
			'     hcRow = dendro_data(as.dendrogram(hclust(dist(ggMat)))) \n',
			'     ggRow = ggplot() + coord_flip() + \n',
			'       geom_segment(data = hcRow$segments, aes(x=x,y=y,xend=xend,yend=yend)) + \n',
			'       scale_y_continuous(breaks = rep(0, uniqueN(ggData$grpBy)), \n',
			'                          labels = unique(ggData$grpBy), expand = c(0, 0)) + \n',
			'       scale_x_continuous(breaks = seq_along(hcRow$labels$label), \n',
			'                          labels = hcRow$labels$label, expand = c(0, 0.5)) + \n',
			'       sctheme(base_size = sList[inpfsz]) + \n',
			'       theme(axis.title = element_blank(), axis.line = element_blank(), \n',
			'             axis.ticks = element_blank(), axis.text.y = element_blank(), \n',
			'             axis.text.x = element_text(color="white", angle = 45, hjust = 1)) \n',
			'     ggData$geneName = factor(ggData$geneName, levels = hcRow$labels$label) \n',
			'   }} else {{ \n',
			'     ggData$geneName = factor(ggData$geneName, levels = rev(geneList$gene)) \n',
			'   }} \n',
			'   if(inpCol){{ \n',
			'     hcCol = dendro_data(as.dendrogram(hclust(dist(t(ggMat))))) \n',
			'     ggCol = ggplot() + \n',
			'       geom_segment(data = hcCol$segments, aes(x=x,y=y,xend=xend,yend=yend)) + \n',
			'       scale_x_continuous(breaks = seq_along(hcCol$labels$label), \n',
			'                          labels = hcCol$labels$label, expand = c(0.05, 0)) + \n',
			'       scale_y_continuous(breaks = rep(0, uniqueN(ggData$geneName)), \n',
			'                          labels = unique(ggData$geneName), expand=c(0,0)) + \n',
			'       sctheme(base_size = sList[inpfsz], Xang = 45, XjusH = 1) + \n',
			'       theme(axis.title = element_blank(), axis.line = element_blank(), \n',
			'             axis.ticks = element_blank(), axis.text.x = element_blank(), \n',
			'             axis.text.y = element_text(color = "white")) \n',
			'     ggData$grpBy = factor(ggData$grpBy, levels = hcCol$labels$label) \n',
			'   }} \n',
   
			'   # Actual plot according to plottype \n',
			'   if(inpPlt == "Bubbleplot"){{ \n',
			'     # Bubbleplot \n',
			' 	ggOut = if (length(splitBy) == 0) ggplot(ggData, aes(grpBy, geneName, color = val, size = prop))\n',
			' 			else ggplot(ggData, aes(grpBy, splitBy, color = val, size = prop)) + ggtitle(geneList$gene)\n',

			'  #   ggOut = ggplot(ggData, aes(grpBy, geneName, color = val, size = prop)) + \n',
			'       ggOut = ggOut + geom_point() +  \n',
			'       sctheme(base_size = sList[inpfsz], Xang = 45, XjusH = 1) +  \n',
			'       scale_x_discrete(expand = c(0.05, 0)) +  \n',
			'       scale_y_discrete(expand = c(0, 0.5)) + \n',
			'       scale_size_continuous("proportion", range = c(0, 8), \n',
			'                             limits = c(0, 1), breaks = c(0.00,0.25,0.50,0.75,1.00)) + \n',
			'       scale_color_gradientn(inpScl, limits = colRange, colours = cList[[inpcols]]) + \n',
			'       guides(color = guide_colorbar(barwidth = 15)) + \n',
			'       theme(axis.title = element_blank(), legend.box = "vertical") \n',
			'   }} else {{ \n',
			'     # Heatmap \n',

			'     ggOut = if (length(splitBy) == 0) ggplot(ggData, aes(grpBy, geneName, fill = val)) \n',
			' 			else ggplot(ggData, aes(grpBy, splitBy, fill = val)) + ggtitle(geneList$gene)\n',
			
			'  #   ggOut = ggplot(ggData, aes(grpBy, geneName, fill = val)) + \n',
			'       ggOut = ggOut + geom_tile() +  \n',
			'       sctheme(base_size = sList[inpfsz], Xang = 45, XjusH = 1) + \n',
			'       scale_x_discrete(expand = c(0.05, 0)) +  \n',
			'       scale_y_discrete(expand = c(0, 0.5)) + \n',
			'       scale_fill_gradientn(inpScl, limits = colRange, colours = cList[[inpcols]]) + \n',
			'       guides(fill = guide_colorbar(barwidth = 15)) + \n',
			'       theme(axis.title = element_blank()) \n',
			'   }} \n',
     
  			' # Final tidy \n',
			'   ggLeg = g_legend(ggOut) \n',
			'   ggOut = ggOut + theme(legend.position = "none") \n',
			'   if(!save){{ \n',
			'     if(inpRow & inpCol){{ggOut =  \n',
			'       grid.arrange(ggOut, ggLeg, ggCol, ggRow, widths = c(7,1), heights = c(1,7,2),  \n',
			'                    layout_matrix = rbind(c(3,NA),c(1,4),c(2,NA)))  \n',
			'     }} else if(inpRow){{ggOut =  \n',
			'       grid.arrange(ggOut, ggLeg, ggRow, widths = c(7,1), heights = c(7,2),  \n',
			'                    layout_matrix = rbind(c(1,3),c(2,NA)))  \n',
			'     }} else if(inpCol){{ggOut =  \n',
			'       grid.arrange(ggOut, ggLeg, ggCol, heights = c(1,7,2),  \n',
			'                    layout_matrix = rbind(c(3),c(1),c(2)))  \n',
			'     }} else {{ggOut =  \n',
			'       grid.arrange(ggOut, ggLeg, heights = c(7,2),  \n',
			'                    layout_matrix = rbind(c(1),c(2)))  \n',
			'     }}  \n',
			'   }} else {{ \n',
			'     if(inpRow & inpCol){{ggOut =  \n',
			'       arrangeGrob(ggOut, ggLeg, ggCol, ggRow, widths = c(7,1), heights = c(1,7,2),  \n',
			'                   layout_matrix = rbind(c(3,NA),c(1,4),c(2,NA)))  \n',
			'     }} else if(inpRow){{ggOut =  \n',
			'       arrangeGrob(ggOut, ggLeg, ggRow, widths = c(7,1), heights = c(7,2),  \n',
			'                   layout_matrix = rbind(c(1,3),c(2,NA)))  \n',
			'     }} else if(inpCol){{ggOut =  \n',
			'       arrangeGrob(ggOut, ggLeg, ggCol, heights = c(1,7,2),  \n',
			'                   layout_matrix = rbind(c(3),c(1),c(2)))  \n',
			'     }} else {{ggOut =  \n',
			'       arrangeGrob(ggOut, ggLeg, heights = c(7,2),  \n',
			'                   layout_matrix = rbind(c(1),c(2)))  \n',
			'     }}  \n',
			'   }} \n',
			'   return(ggOut) \n',
			' }} \n',
			#insert  from SGDDNB/ #75 Violinplot line 638 - 725
			'# Plot gene expression stacked violin / boxplot \n',
             'scStacked = function(inpConf, inpMeta, inp, inpGrp,  \n',
             '                     inpsub1, inpsub2, inpH5,  \n',
             '                     inptyp, inpGene, inpfsz){{ \n',
             '  if(is.null(inpsub1)){{inpsub1 = inpConf$UI[1]}}  \n',
             '  # Identify genes that are in our dataset  \n',
             '  geneList = scGeneList(inp, inpGene)  \n',
             '  geneList = geneList[present == TRUE]  \n',
             '  shiny::validate(need(nrow(geneList) <= 50, "More than 50 genes to plot! Please reduce the gene list!"))  \n',
             '  shiny::validate(need(nrow(geneList) > 1, "Please input at least 2 genes to plot!"))  \n',
             '   \n',
             '  # Prepare ggData  \n',
             '  h5file <- H5File$new(inpH5, mode = "r")  \n',
             '  h5data <- h5file[["grp"]][["data"]]  \n',
             '  ggData = data.table()  \n',
             '  for(iGene in geneList$gene){{  \n',
             '    tmp = inpMeta[, c("sampleID", inpConf[UI == inpsub1]$ID), with = FALSE]  \n',
             '    colnames(tmp) = c("sampleID", "sub")  \n',
             '    tmp$grpBy = inpMeta[[inpConf[UI == inpGrp]$ID]]  \n',
             '    tmp$geneName = iGene  \n',
             '    tmp$val = h5data$read(args = list(inpGene[iGene], quote(expr=)))  \n',
             '    ggData = rbindlist(list(ggData, tmp))  \n',
             '  }}  \n',
             '  h5file$close_all()  \n',
             '  if(length(inpsub2) != 0 & length(inpsub2) != nlevels(ggData$sub)){{  \n',
             '    ggData = ggData[sub %in% inpsub2]  \n',
             '  }}  \n',
             '  shiny::validate(need(uniqueN(ggData$grpBy) > 1, "Only 1 group present, unable to plot!"))  \n',
             '   \n',
             '  ## stacked violine plot \n',
             '   \n',
             '   \n',
             '  if(inptyp=="Stacked Violin"){{ \n',
             '    plot_list<- purrr::map(geneList$gene, function(feature) {{ \n',
             '    ggData_sub = subset(ggData, geneName==feature) \n',
             '      ggplot(ggData_sub, aes(x=grpBy,y=val,fill=grpBy )) +  \n',
             '        geom_violin(scale = "width") + \n',
             '        xlab("") + ylab(feature) + ggtitle("") \n',
             '    }}) \n',
             '  }} else if (inptyp=="Stacked Boxplot"){{ \n',
             '    plot_list<- purrr::map(geneList$gene, function(feature) {{ \n',
             '    ggData_sub = subset(ggData, geneName==feature)  \n',
             '      ggplot(ggData_sub, aes(x=grpBy,y=val,fill=grpBy )) +  \n',
             '        geom_boxplot(outlier.size = 0.5) + \n',
             '        xlab("") + ylab(feature) + ggtitle("") \n',
             '    }}) \n',
             '  }} \n',
             '  ggCol = strsplit(inpConf[UI == inpGrp]$fCL, "\\\\|")[[1]]  \n',
             '  names(ggCol) = levels(ggData$grpBy)  \n',
             '  ggLvl = levels(ggData$grpBy)[levels(ggData$grpBy) %in% unique(ggData$grpBy)]  \n',
             '  ggData$grpBy = factor(ggData$grpBy, levels = ggLvl)  \n',
             '  ggCol = ggCol[ggLvl]  \n',
             '  plot_list = purrr::map(plot_list, function(tmp_plot) {{ \n',
             '    tmp_plot +  \n',
             '      scale_fill_manual(values = ggCol) + \n',
             '      theme_classic() + \n',
             '      theme(legend.position = "none",  \n',
             '            text = element_text(size = sList[inpfsz], family = "Helvetica"), \n',
             '            plot.title= element_blank(), \n',
             '            axis.title.x = element_blank(), \n',
             '            axis.text.x = element_blank(),  \n',
             '            axis.ticks.x = element_blank(),  \n',
             '            axis.title.y = element_text(size = rel(1), angle = 0, vjust = 0.5),  \n',
             '            axis.text.y = element_text(size = rel(1)), \n',
             '            axis.ticks.y = element_line(size = sList[inpfsz] / 20), \n',
             '            plot.margin = unit(c(-0.75, 0, -2, 0), "cm") )  \n',
             '     \n',
             '  }}) \n',
             ' \n',
             '  # Add back x-axis title to bottom plot. patchwork is going to support this? \n',
             '  plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] + \n',
             '    theme(axis.text.x=element_text(angle = 45, hjust = 1, vjust = 1,size = sList[inpfsz]),  \n',
             '          axis.ticks.x = element_line(size = sList[inpfsz] / 20)) \n',
             '   \n',
             '  # change the y-axis tick to only max value  \n',
             '  ymaxs<- purrr::map_dbl(plot_list, function(p){{ \n',
             '    ymax<- max(ggplot_build(p)$layout$panel_scales_y[[1]]$range$range) \n',
             '    ceiling(ymax) \n',
             '  }}) \n',
             '  plot_list<- purrr::map2(plot_list, ymaxs, function(x,y) {{x +  \n',
             '                            scale_y_continuous(breaks = c(y)) +  \n',
             '                            expand_limits(y = y)}}) \n',
             '  p <- patchwork::wrap_plots(plotlist = plot_list, ncol = 1) \n',
             '  p \n',
             '   \n',
             '  return(p) \n',
             '}} \n',
             ' \n',
			 # END #75 line 638 - 725
			 
             ' \n',
             ' \n',
             ' \n',
             ' \n',
             ' \n',
             '### Start server code \n',
             'shinyServer(function(input, output, session) {{ \n',
             '  ### For all tags and Server-side selectize \n',
             '  observe_helpers() \n',
			 'optCrt="{{ option_create: function(data,escape) {{return(\'<div class=\\"create\\"><strong>\' + \'</strong></div>\');}} }}" \n', #PY moved from wrSVmain
             ' \n')
			 
}

#' Write code for main block of server.R
#'
#' @param prefix file prefix 
#'
#' @rdname wrSVmain
#' @export wrSVmain
#'
wrSVmain <- function(prefix, subst = "") {
  glue::glue(#'optCrt="{{ option_create: function(data,escape) {{return(\'<div class=\\"create\\"><strong>\' + \'</strong></div>\');}} }}" \n', #PY moved to wrSVfix
             '  updateSelectizeInput(session, "{prefix}a1inp2", choices = names({prefix}gene), server = TRUE, \n',
             '                       selected = {prefix}def$gene1, options = list( \n',
             '                         maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n',
             '  updateSelectizeInput(session, "{prefix}a3inp1", choices = names({prefix}gene), server = TRUE, \n',
             '                       selected = {prefix}def$gene1, options = list( \n',
             '                         maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n',
             '  updateSelectizeInput(session, "{prefix}a3inp2", choices = names({prefix}gene), server = TRUE, \n',
             '                       selected = {prefix}def$gene2, options = list( \n',
             '                         maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n',
             '  updateSelectizeInput(session, "{prefix}b2inp1", choices = names({prefix}gene), server = TRUE, \n',
             '                       selected = {prefix}def$gene1, options = list( \n',
             '                         maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n',
             '  updateSelectizeInput(session, "{prefix}b2inp2", choices = names({prefix}gene), server = TRUE, \n',
             '                       selected = {prefix}def$gene2, options = list( \n',
             '                         maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n',
             '  updateSelectizeInput(session, "{prefix}c1inp2", server = TRUE, \n',
             '                       choices = c({prefix}conf[is.na(fID)]$UI,names({prefix}gene)), \n',
             '                       selected = {prefix}conf[is.na(fID)]$UI[1], options = list( \n',
             '                         maxOptions = length({prefix}conf[is.na(fID)]$UI) + 3, \n',
             '                         create = TRUE, persist = TRUE, render = I(optCrt))) \n',
			 '	# Dave added following function	for sc1d2inp1			 \n',
			 '	updateSelectizeInput(session, "{prefix}d2inp", choices = names({prefix}gene), server = TRUE,\n', #dave 
			 '							selected = {prefix}def$gene1, options = list(  \n', #dave
             '            				maxOptions = 7, create = TRUE, persist = TRUE, render = I(optCrt))) \n', #dave 
             ' \n',
             ' \n',
             '  ### Plots for tab a1 \n',
             '{subst}  output${prefix}a1sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}a1sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a1sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a1sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}a1oup1 <- renderPlot({{ \n',
             '    scDRcell({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp1,  \n',
             '             input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '             input${prefix}a1siz, input${prefix}a1col1, input${prefix}a1ord1, \n',
             '             input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt, input${prefix}a1lab1) \n',
             '  }}) \n',
             '  output${prefix}a1oup1.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a1oup1", height = pList[input${prefix}a1psz]) \n',
             '  }}) \n',
             '  output${prefix}a1oup1.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a1drX,"_",input${prefix}a1drY,"_",  \n',
             '                                   input${prefix}a1inp1,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a1oup1.h, width = input${prefix}a1oup1.w, useDingbats = FALSE, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp1,   \n',
             '                      input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '                      input${prefix}a1siz, input${prefix}a1col1, input${prefix}a1ord1,  \n',
             '                      input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt, input${prefix}a1lab1) ) \n',
             '  }}) \n',
             '  output${prefix}a1oup1.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a1drX,"_",input${prefix}a1drY,"_",  \n',
             '                                   input${prefix}a1inp1,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a1oup1.h, width = input${prefix}a1oup1.w, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp1,   \n',
             '                      input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '                      input${prefix}a1siz, input${prefix}a1col1, input${prefix}a1ord1,  \n',
             '                      input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt, input${prefix}a1lab1) ) \n',
             '  }}) \n',
             '  output${prefix}a1.dt <- renderDataTable({{ \n',
             '    ggData = scDRnum({prefix}conf, {prefix}meta, input${prefix}a1inp1, input${prefix}a1inp2, \n',
             '                     input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '                     "{prefix}gexpr.h5", {prefix}gene, input${prefix}a1splt) \n',
             '    datatable(ggData, rownames = FALSE, extensions = "Buttons", \n',
             '              options = list(pageLength = -1, dom = "tB", buttons = c("copy", "csv", "excel"))) %>% \n',
             '      formatRound(columns = c("pctExpress"), digits = 2) \n',
             '  }}) \n',
             '   \n',
             '  output${prefix}a1oup2 <- renderPlot({{ \n',
             '    scDRgene({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp2,  \n',
             '             input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '             "{prefix}gexpr.h5", {prefix}gene, \n',
             '             input${prefix}a1siz, input${prefix}a1col2, input${prefix}a1ord2, \n',
             '             input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt) \n',
             '  }}) \n',
             '  output${prefix}a1oup2.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a1oup2", height = pList[input${prefix}a1psz]) \n',
             '  }}) \n',
             '  output${prefix}a1oup2.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a1drX,"_",input${prefix}a1drY,"_",  \n',
             '                                   input${prefix}a1inp2,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a1oup2.h, width = input${prefix}a1oup2.w, useDingbats = FALSE, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp2,  \n',
             '                      input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a1siz, input${prefix}a1col2, input${prefix}a1ord2, \n',
             '                      input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt) ) \n',
             '  }}) \n',
             '  output${prefix}a1oup2.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a1drX,"_",input${prefix}a1drY,"_",  \n',
             '                                   input${prefix}a1inp2,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a1oup2.h, width = input${prefix}a1oup2.w, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a1drX, input${prefix}a1drY, input${prefix}a1inp2,  \n',
             '                      input${prefix}a1sub1, input${prefix}a1sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a1siz, input${prefix}a1col2, input${prefix}a1ord2, \n',
             '                      input${prefix}a1fsz, input${prefix}a1asp, input${prefix}a1txt) ) \n',
             '  }}) \n',
             '   \n',
             '   \n',
             '  ### Plots for tab a2 \n',
             '{subst}  output${prefix}a2sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}a2sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a2sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a2sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}a2oup1 <- renderPlot({{ \n',
             '    scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp1,  \n',
             '             input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '             input${prefix}a2siz, input${prefix}a2col1, input${prefix}a2ord1, \n',
             '             input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab1) \n',
             '  }}) \n',
             '  output${prefix}a2oup1.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a2oup1", height = pList[input${prefix}a2psz]) \n',
             '  }}) \n',
             '  output${prefix}a2oup1.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a2drX,"_",input${prefix}a2drY,"_",  \n',
             '                                   input${prefix}a2inp1,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a2oup1.h, width = input${prefix}a2oup1.w, useDingbats = FALSE, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp1,   \n',
             '                      input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '                      input${prefix}a2siz, input${prefix}a2col1, input${prefix}a2ord1,  \n',
             '                      input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab1) ) \n',
             '  }}) \n',
             '  output${prefix}a2oup1.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a2drX,"_",input${prefix}a2drY,"_",  \n',
             '                                   input${prefix}a2inp1,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a2oup1.h, width = input${prefix}a2oup1.w, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp1,   \n',
             '                      input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '                      input${prefix}a2siz, input${prefix}a2col1, input${prefix}a2ord1,  \n',
             '                      input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab1) ) \n',
             '  }}) \n',
             '   \n',
             '  output${prefix}a2oup2 <- renderPlot({{ \n',
             '    scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp2,  \n',
             '             input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '             input${prefix}a2siz, input${prefix}a2col2, input${prefix}a2ord2, \n',
             '             input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab2) \n',
             '  }}) \n',
             '  output${prefix}a2oup2.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a2oup2", height = pList[input${prefix}a2psz]) \n',
             '  }}) \n',
             '  output${prefix}a2oup2.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a2drX,"_",input${prefix}a2drY,"_",  \n',
             '                                   input${prefix}a2inp2,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a2oup2.h, width = input${prefix}a2oup2.w, useDingbats = FALSE, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp2,   \n',
             '                      input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '                      input${prefix}a2siz, input${prefix}a2col2, input${prefix}a2ord2,  \n',
             '                      input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab2) ) \n',
             '  }}) \n',
             '  output${prefix}a2oup2.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a2drX,"_",input${prefix}a2drY,"_",  \n',
             '                                   input${prefix}a2inp2,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a2oup2.h, width = input${prefix}a2oup2.w, \n',
             '      plot = scDRcell({prefix}conf, {prefix}meta, input${prefix}a2drX, input${prefix}a2drY, input${prefix}a2inp2,   \n',
             '                      input${prefix}a2sub1, input${prefix}a2sub2, \n',
             '                      input${prefix}a2siz, input${prefix}a2col2, input${prefix}a2ord2,  \n',
             '                      input${prefix}a2fsz, input${prefix}a2asp, input${prefix}a2txt, input${prefix}a2lab2) ) \n',
             '  }}) \n',
             '   \n',
             '   \n',
             '  ### Plots for tab a3 \n',
             '{subst}  output${prefix}a3sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a3sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}a3sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a3sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a3sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a3sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}a3sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}a3sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}a3sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}a3oup1 <- renderPlot({{ \n',
             '    scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp1,  \n',
             '             input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '             "{prefix}gexpr.h5", {prefix}gene, \n',
             '             input${prefix}a3siz, input${prefix}a3col1, input${prefix}a3ord1, \n',
             '             input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) \n',
             '  }}) \n',
             '  output${prefix}a3oup1.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a3oup1", height = pList[input${prefix}a3psz]) \n',
             '  }}) \n',
             '  output${prefix}a3oup1.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a3drX,"_",input${prefix}a3drY,"_",  \n',
             '                                   input${prefix}a3inp1,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a3oup1.h, width = input${prefix}a3oup1.w, useDingbats = FALSE, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp1,  \n',
             '                      input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a3siz, input${prefix}a3col1, input${prefix}a3ord1, \n',
             '                      input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) ) \n',
             '  }}) \n',
             '  output${prefix}a3oup1.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a3drX,"_",input${prefix}a3drY,"_",  \n',
             '                                   input${prefix}a3inp1,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a3oup1.h, width = input${prefix}a3oup1.w, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp1,  \n',
             '                      input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a3siz, input${prefix}a3col1, input${prefix}a3ord1, \n',
             '                      input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) ) \n',
             '  }}) \n',
             '   \n',
             '  output${prefix}a3oup2 <- renderPlot({{ \n',
             '    scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp2,  \n',
             '             input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '             "{prefix}gexpr.h5", {prefix}gene, \n',
             '             input${prefix}a3siz, input${prefix}a3col2, input${prefix}a3ord2, \n',
             '             input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) \n',
             '  }}) \n',
             '  output${prefix}a3oup2.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}a3oup2", height = pList[input${prefix}a3psz]) \n',
             '  }}) \n',
             '  output${prefix}a3oup2.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a3drX,"_",input${prefix}a3drY,"_",  \n',
             '                                   input${prefix}a3inp2,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}a3oup2.h, width = input${prefix}a3oup2.w, useDingbats = FALSE, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp2,  \n',
             '                      input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a3siz, input${prefix}a3col2, input${prefix}a3ord2, \n',
             '                      input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) ) \n',
             '  }}) \n',
             '  output${prefix}a3oup2.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}a3drX,"_",input${prefix}a3drY,"_",  \n',
             '                                   input${prefix}a3inp2,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}a3oup2.h, width = input${prefix}a3oup2.w, \n',
             '      plot = scDRgene({prefix}conf, {prefix}meta, input${prefix}a3drX, input${prefix}a3drY, input${prefix}a3inp2,  \n',
             '                      input${prefix}a3sub1, input${prefix}a3sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}a3siz, input${prefix}a3col2, input${prefix}a3ord2, \n',
             '                      input${prefix}a3fsz, input${prefix}a3asp, input${prefix}a3txt) ) \n',
             '  }}) \n',
             '     \n',
             '   \n',
             '  ### Plots for tab b2 \n',
             '{subst}  output${prefix}b2sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}b2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}b2sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}b2sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}b2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}b2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}b2sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}b2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}b2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}b2oup1 <- renderPlot({{ \n',
             '    scDRcoex({prefix}conf, {prefix}meta, input${prefix}b2drX, input${prefix}b2drY,   \n',
             '             input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2sub1, input${prefix}b2sub2, \n',
             '             "{prefix}gexpr.h5", {prefix}gene, \n',
             '             input${prefix}b2siz, input${prefix}b2col1, input${prefix}b2ord1, \n',
             '             input${prefix}b2fsz, input${prefix}b2asp, input${prefix}b2txt) \n',
             '  }}) \n',
             '  output${prefix}b2oup1.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}b2oup1", height = pList2[input${prefix}b2psz]) \n',
             '  }}) \n',
             '  output${prefix}b2oup1.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}b2drX,"_",input${prefix}b2drY,"_",  \n',
             '                                    input${prefix}b2inp1,"_",input${prefix}b2inp2,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}b2oup1.h, width = input${prefix}b2oup1.w, useDingbats = FALSE, \n',
             '      plot = scDRcoex({prefix}conf, {prefix}meta, input${prefix}b2drX, input${prefix}b2drY,  \n',
             '                      input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2sub1, input${prefix}b2sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}b2siz, input${prefix}b2col1, input${prefix}b2ord1, \n',
             '                      input${prefix}b2fsz, input${prefix}b2asp, input${prefix}b2txt) ) \n',
             '  }}) \n',
             '  output${prefix}b2oup1.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}b2drX,"_",input${prefix}b2drY,"_",  \n',
             '                                    input${prefix}b2inp1,"_",input${prefix}b2inp2,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}b2oup1.h, width = input${prefix}b2oup1.w, \n',
             '      plot = scDRcoex({prefix}conf, {prefix}meta, input${prefix}b2drX, input${prefix}b2drY,  \n',
             '                      input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2sub1, input${prefix}b2sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, \n',
             '                      input${prefix}b2siz, input${prefix}b2col1, input${prefix}b2ord1, \n',
             '                      input${prefix}b2fsz, input${prefix}b2asp, input${prefix}b2txt) ) \n',
             '  }}) \n',
             '  output${prefix}b2oup2 <- renderPlot({{ \n',
             '    scDRcoexLeg(input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2col1, input${prefix}b2fsz) \n',
             '  }}) \n',
             '  output${prefix}b2oup2.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}b2oup2", height = "300px") \n',
             '  }}) \n',
             '  output${prefix}b2oup2.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}b2drX,"_",input${prefix}b2drY,"_",  \n',
             '                                    input${prefix}b2inp1,"_",input${prefix}b2inp2,"_leg.pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = 3, width = 4, useDingbats = FALSE, \n',
             '      plot = scDRcoexLeg(input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2col1, input${prefix}b2fsz) ) \n',
             '  }}) \n',
             '  output${prefix}b2oup2.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}b2drX,"_",input${prefix}b2drY,"_",  \n',
             '                                    input${prefix}b2inp1,"_",input${prefix}b2inp2,"_leg.png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = 3, width = 4, \n',
             '      plot = scDRcoexLeg(input${prefix}b2inp1, input${prefix}b2inp2, input${prefix}b2col1, input${prefix}b2fsz) ) \n',
             '  }}) \n',
             '  output${prefix}b2.dt <- renderDataTable({{ \n',
             '    ggData = scDRcoexNum({prefix}conf, {prefix}meta, input${prefix}b2inp1, input${prefix}b2inp2, \n',
             '                         input${prefix}b2sub1, input${prefix}b2sub2, "{prefix}gexpr.h5", {prefix}gene) \n',
             '    datatable(ggData, rownames = FALSE, extensions = "Buttons", \n',
             '              options = list(pageLength = -1, dom = "tB", buttons = c("copy", "csv", "excel"))) %>% \n',
             '      formatRound(columns = c("percent"), digits = 2) \n',
             '  }}) \n',
             '     \n',
             '   \n',
             '  ### Plots for tab c1 \n',
             '{subst}  output${prefix}c1sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}c1sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}c1sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}c1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}c1sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}c1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}c1oup <- renderPlot({{ \n',
             '    scVioBox({prefix}conf, {prefix}meta, input${prefix}c1inp1, input${prefix}c1inp2, \n',
             '             input${prefix}c1sub1, input${prefix}c1sub2, \n',
             '             "{prefix}gexpr.h5", {prefix}gene, input${prefix}c1typ, input${prefix}c1pts, \n',
             '             input${prefix}c1siz, input${prefix}c1fsz) \n',
             '  }}) \n',
             '  output${prefix}c1oup.ui <- renderUI({{ \n',
             '    plotOutput("{prefix}c1oup", height = pList2[input${prefix}c1psz]) \n',
             '  }}) \n',
             '  output${prefix}c1oup.pdf <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}c1typ,"_",input${prefix}c1inp1,"_",  \n',
             '                                   input${prefix}c1inp2,".pdf") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "pdf", height = input${prefix}c1oup.h, width = input${prefix}c1oup.w, useDingbats = FALSE, \n',
             '      plot = scVioBox({prefix}conf, {prefix}meta, input${prefix}c1inp1, input${prefix}c1inp2, \n',
             '                      input${prefix}c1sub1, input${prefix}c1sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, input${prefix}c1typ, input${prefix}c1pts, \n',
             '                      input${prefix}c1siz, input${prefix}c1fsz) ) \n',
             '  }}) \n',
             '  output${prefix}c1oup.png <- downloadHandler( \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}c1typ,"_",input${prefix}c1inp1,"_",  \n',
             '                                   input${prefix}c1inp2,".png") }}, \n',
             '    content = function(file) {{ ggsave( \n',
             '      file, device = "png", height = input${prefix}c1oup.h, width = input${prefix}c1oup.w, \n',
             '      plot = scVioBox({prefix}conf, {prefix}meta, input${prefix}c1inp1, input${prefix}c1inp2, \n',
             '                      input${prefix}c1sub1, input${prefix}c1sub2, \n',
             '                      "{prefix}gexpr.h5", {prefix}gene, input${prefix}c1typ, input${prefix}c1pts, \n',
             '                      input${prefix}c1siz, input${prefix}c1fsz) ) \n',
             '  }}) \n',
             '     \n',
             '   \n', 
             '### Plots for tab c2 \n',
             '{subst}  output${prefix}c2sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}c2sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}c2sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}c2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}c2sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}c2sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}c2sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             'output${prefix}c2oup <- renderPlot({{ \n',
             '  scProp({prefix}conf, {prefix}meta, input${prefix}c2inp1, input${prefix}c2inp2,  \n',
             '         input${prefix}c2sub1, input${prefix}c2sub2, \n',
             '         input${prefix}c2typ, input${prefix}c2flp, input${prefix}c2fsz) \n',
             '}}) \n',
             'output${prefix}c2oup.ui <- renderUI({{ \n',
             '  plotOutput("{prefix}c2oup", height = pList2[input${prefix}c2psz]) \n',
             '}}) \n',
             'output${prefix}c2oup.pdf <- downloadHandler( \n',
             '  filename = function() {{ paste0("{prefix}",input${prefix}c2typ,"_",input${prefix}c2inp1,"_",  \n',
             '                                 input${prefix}c2inp2,".pdf") }}, \n',
             '  content = function(file) {{ ggsave( \n',
             '    file, device = "pdf", height = input${prefix}c2oup.h, width = input${prefix}c2oup.w, useDingbats = FALSE, \n',
             '    plot = scProp({prefix}conf, {prefix}meta, input${prefix}c2inp1, input${prefix}c2inp2,  \n',
             '                  input${prefix}c2sub1, input${prefix}c2sub2, \n',
             '                  input${prefix}c2typ, input${prefix}c2flp, input${prefix}c2fsz) ) \n',
             '  }}) \n',
             'output${prefix}c2oup.png <- downloadHandler( \n',
             '  filename = function() {{ paste0("{prefix}",input${prefix}c2typ,"_",input${prefix}c2inp1,"_",  \n',
             '                                 input${prefix}c2inp2,".png") }}, \n',
             '  content = function(file) {{ ggsave( \n',
             '    file, device = "png", height = input${prefix}c2oup.h, width = input${prefix}c2oup.w, \n',
             '    plot = scProp({prefix}conf, {prefix}meta, input${prefix}c2inp1, input${prefix}c2inp2,  \n',
             '                  input${prefix}c2sub1, input${prefix}c2sub2, \n',
             '                  input${prefix}c2typ, input${prefix}c2flp, input${prefix}c2fsz) ) \n',
             '  }}) \n',
             '     \n',
             '   \n', 
             '  ### Plots for tab d1 \n',
             '{subst}  output${prefix}d1sub1.ui <- renderUI({{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}d1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    checkboxGroupInput("{prefix}d1sub2", "Select which cells to show", inline = TRUE, \n',
             '{subst}                       choices = sub, selected = sub) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}d1sub1non, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}d1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}d1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = NULL, inline = TRUE) \n',
             '{subst}  }}) \n',
             '{subst}  observeEvent(input${prefix}d1sub1all, {{ \n',
             '{subst}    sub = strsplit({prefix}conf[UI == input${prefix}d1sub1]$fID, "\\\\|")[[1]] \n',
             '{subst}    updateCheckboxGroupInput(session, inputId = "{prefix}d1sub2", label = "Select which cells to show", \n',
             '{subst}                             choices = sub, selected = sub, inline = TRUE) \n',
             '{subst}  }}) \n',
             '  output${prefix}d1oupTxt <- renderUI({{ \n',
             '    geneList = scGeneList(input${prefix}d1inp, {prefix}gene) \n',
             '    if(nrow(geneList) > 50){{ \n',
             '      HTML("More than 50 input genes! Please reduce the gene list!") \n',
             '    }} else {{ \n',
             '      oup = paste0(nrow(geneList[present == TRUE]), " genes OK and will be plotted") \n',
             '      if(nrow(geneList[present == FALSE]) > 0){{ \n',
             '        oup = paste0(oup, "<br/>", \n',
             '                     nrow(geneList[present == FALSE]), " genes not found (", \n',
             '                     paste0(geneList[present == FALSE]$gene, collapse = ", "), ")") \n',
             '      }} \n',
             '      HTML(oup) \n',
             '    }} \n',
             '  }}) \n',
             '  output${prefix}d1oup <- renderPlot({{ \n',
			 #Deleted content from #75
             # '    scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt, \n',
             # '               input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene, \n',
             # '               input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col, \n',
             # '               input${prefix}d1cols, input${prefix}d1fsz) \n',
             # '  }}) \n',
             # '  output${prefix}d1oup.ui <- renderUI({{ \n',
             # '    plotOutput("{prefix}d1oup", height = pList3[input${prefix}d1psz]) \n',
             # '  }}) \n',
             # '  output${prefix}d1oup.pdf <- downloadHandler( \n',
             # '    filename = function() {{ paste0("{prefix}",input${prefix}d1plt,"_",input${prefix}d1grp,".pdf") }}, \n',
             # '    content = function(file) {{ ggsave( \n',
             # '      file, device = "pdf", height = input${prefix}d1oup.h, width = input${prefix}d1oup.w, \n',
             # '      plot = scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt, \n',
             # '                        input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene, \n',
             # '                        input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col, \n',
             # '                        input${prefix}d1cols, input${prefix}d1fsz, save = TRUE) ) \n',
             # '  }}) \n',
             # '  output${prefix}d1oup.png <- downloadHandler( \n',
             # '    filename = function() {{ paste0("{prefix}",input${prefix}d1plt,"_",input${prefix}d1grp,".png") }}, \n',
             # '    content = function(file) {{ ggsave( \n',
             # '      file, device = "png", height = input${prefix}d1oup.h, width = input${prefix}d1oup.w, \n',
             # '      plot = scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt, \n',
             # '                        input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene, \n',
             # '                        input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col, \n',
             # '                        input${prefix}d1cols, input${prefix}d1fsz, save = TRUE) ) \n',
             # '  }}) \n',
             # '     \n',
             # '   \n',             
			#copied #75 part 2
			'    if(input${prefix}d1plt %in% c("Bubbleplot", "Heatmap")){{ \n',
             '        scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt,  \n',
             '             input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '             input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col,  \n',
             '             input${prefix}d1cols, input${prefix}d1fsz)  \n',
             '    }} else {{ \n',
             '        scStacked({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp,  \n',
             '             input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5",  \n',
             '             input${prefix}d1plt, {prefix}gene, input${prefix}d1fsz) \n',
             '    }} \n',
             '  }})  \n',
             '  output${prefix}d1oup.ui <- renderUI({{  \n',
             '    plotOutput("{prefix}d1oup", height = pList3[input${prefix}d1psz])  \n',
             '  }})  \n',
             '  output${prefix}d1oup.pdf <- downloadHandler(  \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}d1plt,"_",input${prefix}d1grp,".pdf") }},  \n',
             '    content = function(file) {{ ggsave(  \n',
             '      file, device = "pdf", height = input${prefix}d1oup.h, width = input${prefix}d1oup.w,  \n',
             '      plot =  if(input${prefix}d1plt %in% c("Bubbleplot", "Heatmap")){{ \n',
             '                  scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt,  \n',
             '                       input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '                       input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col,  \n',
             '                       input${prefix}d1cols, input${prefix}d1fsz)  \n',
             '              }} else {{ \n',
             '                  scStacked({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp,  \n',
             '                       input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5",  \n',
             '                       input${prefix}d1plt, {prefix}gene, input${prefix}d1fsz) \n',
             '              }}) \n',
             '  }})  \n',
             '  output${prefix}d1oup.png <- downloadHandler(  \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}d1plt,"_",input${prefix}d1grp,".png") }},  \n',
             '    content = function(file) {{ ggsave(  \n',
             '      file, device = "png", height = input${prefix}d1oup.h, width = input${prefix}d1oup.w,  \n',
             '      plot =  if(input${prefix}d1plt %in% c("Bubbleplot", "Heatmap")){{ \n',
             '                  scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp, input${prefix}d1plt,  \n',
             '                       input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '                       input${prefix}d1scl, input${prefix}d1row, input${prefix}d1col,  \n',
             '                       input${prefix}d1cols, input${prefix}d1fsz)  \n',
             '              }} else {{ \n',
             '                  scStacked({prefix}conf, {prefix}meta, input${prefix}d1inp, input${prefix}d1grp,  \n',
             '                       input${prefix}d1sub1, input${prefix}d1sub2, "{prefix}gexpr.h5",  \n',
             '                       input${prefix}d1plt, {prefix}gene, input${prefix}d1fsz) \n',
             '              }}) \n',
             '  }})  \n',
			#end copied #75 part 2
             '    ### Plots for tab d2   DAVE  \n\n',
  
   
             '    output${prefix}d2sub1.ui <- renderUI({{  \n',
             '    sub = strsplit({prefix}conf[UI == input${prefix}d2sub1]$fID, "\\\\|")[[1]]  \n',
             '    checkboxGroupInput("{prefix}d2sub2", "Select which cells to show", inline = TRUE,  \n',
             '                       choices = sub, selected = sub)  \n',
             '  }})  \n',
             '  observeEvent(input${prefix}d2sub1non, {{  \n',
             '    sub = strsplit({prefix}conf[UI == input${prefix}d2sub1]$fID, "\\\\|")[[1]]  \n',
             '    updateCheckboxGroupInput(session, inputId = "{prefix}d2sub2", label = "Select which cells to show",  \n',
             '                             choices = sub, selected = NULL, inline = TRUE)  \n',
             '  }})  \n',
             '  observeEvent(input${prefix}d2sub1all, {{  \n',
             '    sub = strsplit({prefix}conf[UI == input${prefix}d2sub1]$fID, "\\\\|")[[1]]  \n',
             '    updateCheckboxGroupInput(session, inputId = "{prefix}d2sub2", label = "Select which cells to show",  \n',
             '                             choices = sub, selected = sub, inline = TRUE)  \n',
             '  }})  \n',
             '  output${prefix}d2oupTxt <- renderUI({{  \n',
             '    geneList = scGeneList(input${prefix}d2inp, {prefix}gene)  \n',
             '    if(nrow(geneList) > 50){{ \n',
             '	  HTML("More than 50 input genes! Please reduce the gene list!")  \n',
             '    }} else {{  \n',
             '      oup = paste0(nrow(geneList[present == TRUE]), " genes OK and will be plotted")  \n',
             '      if(nrow(geneList[present == FALSE]) > 0){{  \n',
             '        oup = paste0(oup, "<br/>",  \n',
             '                     nrow(geneList[present == FALSE]), " genes not found (",  \n',
             '                     paste0(geneList[present == FALSE]$gene, collapse = ", "), ")")  \n',
             '      }}  \n',
             '      #HTML(oup)  \n',
             '	  HTML("") \n',
             '    }}  \n',
             '  }})  \n',
             '  output${prefix}d2oup <- renderPlot({{  \n',
             '    scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d2inp, input${prefix}d2grp, input${prefix}d2plt,  \n',
             '               input${prefix}d2sub1, input${prefix}d2sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '               input${prefix}d2scl, input${prefix}d2row, input${prefix}d2col,  \n',
             '               input${prefix}d2cols, input${prefix}d2fsz, splitBy=input${prefix}d2split)  \n',
             '  }})  \n',
             '  output${prefix}d2oup.ui <- renderUI({{  \n',
             '    plotOutput("{prefix}d2oup", height = pList3[input${prefix}d2psz])  \n',
             '  }})  \n',
             '  output${prefix}d2oup.pdf <- downloadHandler(  \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}d2plt,"_",input${prefix}d2grp,".pdf") }},  \n',
             '    content = function(file) {{ ggsave(  \n',
             '      file, device = "pdf", height = input${prefix}d2oup.h, width = input${prefix}d2oup.w,  \n',
             '      plot = scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d2inp, input${prefix}d2grp, input${prefix}d2plt,  \n',
             '                        input${prefix}d2sub1, input${prefix}d2sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '                        input${prefix}d2scl, input${prefix}d2row, input${prefix}d2col,  \n',
             '                        input${prefix}d2cols, input${prefix}d2fsz, save = TRUE, splitBy=input${prefix}d2split) )  \n',
             '  }})  \n',
             '  output${prefix}d2oup.png <- downloadHandler(  \n',
             '    filename = function() {{ paste0("{prefix}",input${prefix}d2plt,"_",input${prefix}d2grp,".png") }},  \n',
             '    content = function(file) {{ ggsave(  \n',
             '      file, device = "png", height = input${prefix}d2oup.h, width = input${prefix}d2oup.w,  \n',
             '      plot = scBubbHeat({prefix}conf, {prefix}meta, input${prefix}d2inp, input${prefix}d2grp, input${prefix}d2plt,  \n',
             '                        input${prefix}d2sub1, input${prefix}d2sub2, "{prefix}gexpr.h5", {prefix}gene,  \n',
             '                        input${prefix}d2scl, input${prefix}d2row, input${prefix}d2col,  \n',
             '                        input${prefix}d2cols, input${prefix}d2fsz, save = TRUE, splitBy=input${prefix}d2split) ) \n',
             
			 
          
			'  }}) \n',#close server function
             '   \n',
             '   \n',
             '   \n')
}

#' Write code for final portion of server.R
#'
#' @rdname wrSVend
#' @export wrSVend
#'
wrSVend <- function() {
  glue::glue('   \n',
             '   \n',
             '}}) \n',
             ' \n',
             ' \n',
             ' \n',
             ' \n')
}

#' Write code for loading objects for ui.R
#'
#' @param prefix file prefix 
#'
#' @rdname wrUIload
#' @export wrUIload
#'
wrUIload <- function(prefix) {
  glue::glue('{prefix}conf = readRDS("{prefix}conf.rds")\n',
             '{prefix}def  = readRDS("{prefix}def.rds")\n',
             '\n\n\n\n')
}

#' Write code for front portion of ui.R
#'
#' @param title shiny app title
#' @param ganalytics Google analytics tracking ID (e.g. "UA-123456789-0")
#'
#' @rdname wrUIsingle
#' @export wrUIsingle
#'
wrUIsingle <- function(title, ganalytics) {
  if(!is.na(ganalytics)){
    ga = 'tags$head(includeHTML(("google-analytics.html"))),'
  } else {
    ga = ''
  }
  glue::glue('### Start server code \n',
             'shinyUI(fluidPage( \n',
             '### HTML formatting of error messages \n',
             '{ga} \n',
             'tags$head(tags$style(HTML(".shiny-output-error-validation {{color: red; font-weight: bold;}}"))), \n',
             'list(tags$style(HTML(".navbar-default .navbar-nav {{ font-weight: bold; font-size: 16px; }}"))), \n',
             ' \n',
             '   \n',
             '### Page title \n',
             'titlePanel("{title}"),  \n',
             'navbarPage( \n',
             '  NULL,  \n',
             ' \n')
}

#' Write code for main block of ui.R
#'
#' @param prefix file prefix 
#'
#' @rdname wrUImain
#' @export wrUImain
#'
wrUImain <- function(prefix, subst = "", ptsiz = "1.25") {
  glue::glue('  ### Tab1.a1: cellInfo vs geneExpr on dimRed \n',
             '  tabPanel( \n',
             '    HTML("CellInfo vs GeneExpr"), \n',
             '    h4("Cell information vs gene expression on reduced dimensions"), \n',
             '    "In this tab, users can visualise both cell information and gene ",  \n',
             '    "expression side-by-side on low-dimensional representions.", \n',
             '    br(),br(), \n',
             '    fluidRow( \n',
             '      column( \n',
             '        3, h4("Dimension Reduction"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            12, selectInput("{prefix}a1drX", "X-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                           selected = {prefix}def$dimred[1]), \n',
             '            selectInput("{prefix}a1drY", "Y-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                        selected = {prefix}def$dimred[2])) \n',
             '        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        3{subst}, actionButton("{prefix}a1togL", "Toggle to subset cells"), \n',
             '{subst}        conditionalPanel( \n',
             '{subst}          condition = "input.{prefix}a1togL % 2 == 1", \n',
             '{subst}          selectInput("{prefix}a1sub1", "Cell information to subset:", \n',
             '{subst}                      choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                      selected = {prefix}def$grp1), \n',
             '{subst}          uiOutput("{prefix}a1sub1.ui"), \n',
             '{subst}          actionButton("{prefix}a1sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}          actionButton("{prefix}a1sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, actionButton("{prefix}a1tog0", "Toggle graphics controls"), \n',
             '        conditionalPanel( \n',
             '          condition = "input.{prefix}a1tog0 % 2 == 1", \n',
             '          fluidRow( \n',
             '            column( \n',
             '              6, sliderInput("{prefix}a1siz", "Point size:", \n',
             '                             min = 0, max = 4, value = {ptsiz}, step = 0.25), \n',
             '              radioButtons("{prefix}a1psz", "Plot size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE), \n',
             '              radioButtons("{prefix}a1fsz", "Font size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE) \n',
             '            ), \n',
             '            column( \n',
             '              6, radioButtons("{prefix}a1asp", "Aspect ratio:", \n',
             '                              choices = c("Square", "Fixed", "Free"), \n',
             '                              selected = "Square", inline = TRUE), \n',
             '              checkboxInput("{prefix}a1txt", "Show axis text", value = FALSE) \n',
             '            ) \n',
             '          ) \n',
             '        ) \n',
             '      )  # End of column (6 space) \n',
             '    ),   # End of fluidRow (4 space) \n',
             '    fluidRow( \n',
             '      column( \n',
             '        6, style="border-right: 2px solid black", h4("Cell information"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a1inp1", "Cell information:", \n',
             '                           choices = {prefix}conf$UI, \n',
             '                           selected = {prefix}def$meta1) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Cell information to colour cells by", \n',
             '                     content = c("Select cell information to colour cells", \n',
             '                                 "- Categorical covariates have a fixed colour palette", \n',
             '                                 paste0("- Continuous covariates are coloured in a ",  \n',
             '                                        "Blue-Yellow-Red colour scheme, which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a1tog1", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a1tog1 % 2 == 1", \n',
             '              radioButtons("{prefix}a1col1", "Colour (Continuous data):", \n',
             '                           choices = c("White-Red","Blue-Yellow-Red","Yellow-Green-Purple"), \n',
             '                           selected = "Blue-Yellow-Red"), \n',
             '              radioButtons("{prefix}a1ord1", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Original", inline = TRUE), \n',
             '              checkboxInput("{prefix}a1lab1", "Show cell info labels", value = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ), \n',
             '        fluidRow(column(12, uiOutput("{prefix}a1oup1.ui"))), \n',
             '        downloadButton("{prefix}a1oup1.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a1oup1.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a1oup1.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a1oup1.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)), br(), \n',
             '        actionButton("{prefix}a1tog9", "Toggle to show cell numbers / statistics"), \n',
             '        conditionalPanel( \n',
             '          condition = "input.{prefix}a1tog9 % 2 == 1", \n',
             '          h4("Cell numbers / statistics"), \n',
             '          radioButtons("{prefix}a1splt", "Split continuous cell info into:", \n',
             '                       choices = c("Quartile", "Decile"), \n',
             '                       selected = "Decile", inline = TRUE), \n',
             '          dataTableOutput("{prefix}a1.dt") \n',
             '        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, h4("Gene expression"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a1inp2", "Gene name:", choices=NULL) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Gene expression to colour cells by", \n',
             '                     content = c("Select gene to colour cells by gene expression", \n',
             '                                 paste0("- Gene expression are coloured in a ", \n',
             '                                        "White-Red colour scheme which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a1tog2", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a1tog2 % 2 == 1", \n',
             '              radioButtons("{prefix}a1col2", "Colour:", \n',
             '                           choices = c("White-Red","Blue-Yellow-Red","Yellow-Green-Purple"), \n',
             '                           selected = "White-Red"), \n',
             '              radioButtons("{prefix}a1ord2", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Max-1st", inline = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ) , \n',
             '        fluidRow(column(12, uiOutput("{prefix}a1oup2.ui"))), \n',
             '        downloadButton("{prefix}a1oup2.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a1oup2.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a1oup2.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a1oup2.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)) \n',
             '      )  # End of column (6 space) \n',
             '    )    # End of fluidRow (4 space) \n',
             '  ),     # End of tab (2 space) \n',
             ' \n',
             '  ### Tab1.a2: cellInfo vs cellInfo on dimRed \n',
             '  tabPanel( \n',
             '    HTML("CellInfo vs CellInfo"), \n',
             '    h4("Cell information vs cell information on dimension reduction"), \n',
             '    "In this tab, users can visualise two cell informations side-by-side ", \n',
             '    "on low-dimensional representions.", \n',
             '    br(),br(), \n',
             '    fluidRow( \n',
             '      column( \n',
             '        3, h4("Dimension Reduction"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            12, selectInput("{prefix}a2drX", "X-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                           selected = {prefix}def$dimred[1]), \n',
             '            selectInput("{prefix}a2drY", "Y-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                        selected = {prefix}def$dimred[2])) \n',
             '        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        3{subst}, actionButton("{prefix}a2togL", "Toggle to subset cells"), \n',
             '{subst}        conditionalPanel( \n',
             '{subst}          condition = "input.{prefix}a2togL % 2 == 1", \n',
             '{subst}          selectInput("{prefix}a2sub1", "Cell information to subset:", \n',
             '{subst}                      choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                      selected = {prefix}def$grp1), \n',
             '{subst}          uiOutput("{prefix}a2sub1.ui"), \n',
             '{subst}          actionButton("{prefix}a2sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}          actionButton("{prefix}a2sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, actionButton("{prefix}a2tog0", "Toggle graphics controls"), \n',
             '        conditionalPanel( \n',
             '          condition = "input.{prefix}a2tog0 % 2 == 1", \n',
             '          fluidRow( \n',
             '            column( \n',
             '              6, sliderInput("{prefix}a2siz", "Point size:", \n',
             '                             min = 0, max = 4, value = {ptsiz}, step = 0.25), \n',
             '              radioButtons("{prefix}a2psz", "Plot size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE), \n',
             '              radioButtons("{prefix}a2fsz", "Font size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE) \n',
             '            ), \n',
             '            column( \n',
             '              6, radioButtons("{prefix}a2asp", "Aspect ratio:", \n',
             '                              choices = c("Square", "Fixed", "Free"), \n',
             '                              selected = "Square", inline = TRUE), \n',
             '              checkboxInput("{prefix}a2txt", "Show axis text", value = FALSE) \n',
             '            ) \n',
             '          ) \n',
             '        ) \n',
             '      )  # End of column (6 space) \n',
             '    ),   # End of fluidRow (4 space) \n',
             '    fluidRow( \n',
             '      column( \n',
             '        6, style="border-right: 2px solid black", h4("Cell information 1"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a2inp1", "Cell information:", \n',
             '                           choices = {prefix}conf$UI, \n',
             '                           selected = {prefix}def$meta1) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Cell information to colour cells by", \n',
             '                     content = c("Select cell information to colour cells", \n',
             '                                 "- Categorical covariates have a fixed colour palette", \n',
             '                                 paste0("- Continuous covariates are coloured in a ",  \n',
             '                                        "Blue-Yellow-Red colour scheme, which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a2tog1", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a2tog1 % 2 == 1", \n',
             '              radioButtons("{prefix}a2col1", "Colour (Continuous data):", \n',
             '                           choices = c("White-Red", "Blue-Yellow-Red", \n',
             '                                       "Yellow-Green-Purple"), \n',
             '                           selected = "Blue-Yellow-Red"), \n',
             '              radioButtons("{prefix}a2ord1", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Original", inline = TRUE), \n',
             '              checkboxInput("{prefix}a2lab1", "Show cell info labels", value = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ), \n',
             '        fluidRow(column(12, uiOutput("{prefix}a2oup1.ui"))), \n',
             '        downloadButton("{prefix}a2oup1.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a2oup1.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a2oup1.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a2oup1.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, h4("Cell information 2"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a2inp2", "Cell information:", \n',
             '                           choices = {prefix}conf$UI, \n',
             '                           selected = {prefix}def$meta2) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Cell information to colour cells by", \n',
             '                     content = c("Select cell information to colour cells", \n',
             '                                 "- Categorical covariates have a fixed colour palette", \n',
             '                                 paste0("- Continuous covariates are coloured in a ",  \n',
             '                                        "Blue-Yellow-Red colour scheme, which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a2tog2", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a2tog2 % 2 == 1", \n',
             '              radioButtons("{prefix}a2col2", "Colour (Continuous data):", \n',
             '                           choices = c("White-Red", "Blue-Yellow-Red", \n',
             '                                       "Yellow-Green-Purple"), \n',
             '                           selected = "Blue-Yellow-Red"), \n',
             '              radioButtons("{prefix}a2ord2", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Original", inline = TRUE), \n',
             '              checkboxInput("{prefix}a2lab2", "Show cell info labels", value = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ), \n',
             '        fluidRow(column(12, uiOutput("{prefix}a2oup2.ui"))), \n',
             '        downloadButton("{prefix}a2oup2.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a2oup2.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a2oup2.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a2oup2.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)) \n',
             '      )  # End of column (6 space) \n',
             '    )    # End of fluidRow (4 space) \n',
             '  ),     # End of tab (2 space) \n',
             '   \n',
             '  ### Tab1.a3: geneExpr vs geneExpr on dimRed \n',
             '  tabPanel( \n',
             '    HTML("GeneExpr vs GeneExpr"), \n',
             '    h4("Gene expression vs gene expression on dimension reduction"), \n',
             '    "In this tab, users can visualise two gene expressions side-by-side ", \n',
             '    "on low-dimensional representions.", \n',
             '    br(),br(), \n',
             '    fluidRow( \n',
             '      column( \n',
             '        3, h4("Dimension Reduction"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            12, selectInput("{prefix}a3drX", "X-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                           selected = {prefix}def$dimred[1]), \n',
             '            selectInput("{prefix}a3drY", "Y-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                        selected = {prefix}def$dimred[2])) \n',
             '        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        3{subst}, actionButton("{prefix}a3togL", "Toggle to subset cells"), \n',
             '{subst}        conditionalPanel( \n',
             '{subst}          condition = "input.{prefix}a3togL % 2 == 1", \n',
             '{subst}          selectInput("{prefix}a3sub1", "Cell information to subset:", \n',
             '{subst}                      choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                      selected = {prefix}def$grp1), \n',
             '{subst}          uiOutput("{prefix}a3sub1.ui"), \n',
             '{subst}          actionButton("{prefix}a3sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}          actionButton("{prefix}a3sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}        ) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, actionButton("{prefix}a3tog0", "Toggle graphics controls"), \n',
             '        conditionalPanel( \n',
             '          condition = "input.{prefix}a3tog0 % 2 == 1", \n',
             '          fluidRow( \n',
             '            column( \n',
             '              6, sliderInput("{prefix}a3siz", "Point size:", \n',
             '                             min = 0, max = 4, value = {ptsiz}, step = 0.25), \n',
             '              radioButtons("{prefix}a3psz", "Plot size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE), \n',
             '              radioButtons("{prefix}a3fsz", "Font size:", \n',
             '                           choices = c("Small", "Medium", "Large"), \n',
             '                           selected = "Medium", inline = TRUE) \n',
             '            ), \n',
             '            column( \n',
             '              6, radioButtons("{prefix}a3asp", "Aspect ratio:", \n',
             '                              choices = c("Square", "Fixed", "Free"), \n',
             '                              selected = "Square", inline = TRUE), \n',
             '              checkboxInput("{prefix}a3txt", "Show axis text", value = FALSE) \n',
             '            ) \n',
             '          ) \n',
             '        ) \n',
             '      )  # End of column (6 space) \n',
             '    ),   # End of fluidRow (4 space) \n',
             '    fluidRow( \n',
             '      column( \n',
             '        6, style="border-right: 2px solid black", h4("Gene expression 1"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a3inp1", "Gene name:", choices=NULL) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Gene expression to colour cells by", \n',
             '                     content = c("Select gene to colour cells by gene expression", \n',
             '                                 paste0("- Gene expression are coloured in a ", \n',
             '                                        "White-Red colour scheme which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a3tog1", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a3tog1 % 2 == 1", \n',
             '              radioButtons("{prefix}a3col1", "Colour:", \n',
             '                           choices = c("White-Red", "Blue-Yellow-Red", \n',
             '                                       "Yellow-Green-Purple"), \n',
             '                           selected = "White-Red"), \n',
             '              radioButtons("{prefix}a3ord1", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Max-1st", inline = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ), \n',
             '        fluidRow(column(12, uiOutput("{prefix}a3oup1.ui"))), \n',
             '        downloadButton("{prefix}a3oup1.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a3oup1.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a3oup1.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a3oup1.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)) \n',
             '      ), # End of column (6 space) \n',
             '      column( \n',
             '        6, h4("Gene expression 2"), \n',
             '        fluidRow( \n',
             '          column( \n',
             '            6, selectInput("{prefix}a3inp2", "Gene name:", choices=NULL) %>%  \n',
             '              helper(type = "inline", size = "m", fade = TRUE, \n',
             '                     title = "Gene expression to colour cells by", \n',
             '                     content = c("Select gene to colour cells by gene expression", \n',
             '                                 paste0("- Gene expression are coloured in a ", \n',
             '                                        "White-Red colour scheme which can be ", \n',
             '                                        "changed in the plot controls"))) \n',
             '          ), \n',
             '          column( \n',
             '            6, actionButton("{prefix}a3tog2", "Toggle plot controls"), \n',
             '            conditionalPanel( \n',
             '              condition = "input.{prefix}a3tog2 % 2 == 1", \n',
             '              radioButtons("{prefix}a3col2", "Colour:", \n',
             '                           choices = c("White-Red", "Blue-Yellow-Red", \n',
             '                                       "Yellow-Green-Purple"), \n',
             '                           selected = "White-Red"), \n',
             '              radioButtons("{prefix}a3ord2", "Plot order:", \n',
             '                           choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                           selected = "Max-1st", inline = TRUE) \n',
             '            ) \n',
             '          ) \n',
             '        ), \n',
             '        fluidRow(column(12, uiOutput("{prefix}a3oup2.ui"))), \n',
             '        downloadButton("{prefix}a3oup2.pdf", "Download PDF"), \n',
             '        downloadButton("{prefix}a3oup2.png", "Download PNG"), br(), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a3oup2.h", "PDF / PNG height:", width = "138px", \n',
             '                         min = 4, max = 20, value = 6, step = 0.5)), \n',
             '        div(style="display:inline-block", \n',
             '            numericInput("{prefix}a3oup2.w", "PDF / PNG width:", width = "138px", \n',
             '                         min = 4, max = 20, value = 8, step = 0.5)) \n',
             '      )  # End of column (6 space) \n',
             '    )    # End of fluidRow (4 space) \n',
             '  ),     # End of tab (2 space) \n',
             ' \n',
             ' ### Tab1.b2: Gene coexpression plot \n',
             ' tabPanel( \n',
             '   HTML("Gene coexpression"), \n',
             '   h4("Coexpression of two genes on reduced dimensions"), \n',
             '   "In this tab, users can visualise the coexpression of two genes ", \n',
             '   "on low-dimensional representions.", \n',
             '   br(),br(), \n',
             '   fluidRow( \n',
             '     column( \n',
             '       3, h4("Dimension Reduction"), \n',
             '       fluidRow( \n',
             '         column( \n',
             '           12, selectInput("{prefix}b2drX", "X-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                           selected = {prefix}def$dimred[1]), \n',
             '           selectInput("{prefix}b2drY", "Y-axis:", choices = {prefix}conf[dimred == TRUE]$UI, \n',
             '                       selected = {prefix}def$dimred[2])) \n',
             '       ) \n',
             '     ), # End of column (6 space) \n',
             '     column( \n',
             '       3{subst}, actionButton("{prefix}b2togL", "Toggle to subset cells"), \n',
             '{subst}       conditionalPanel( \n',
             '{subst}         condition = "input.{prefix}b2togL % 2 == 1", \n',
             '{subst}         selectInput("{prefix}b2sub1", "Cell information to subset:", \n',
             '{subst}                     choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                    selected = {prefix}def$grp1), \n',
             '{subst}         uiOutput("{prefix}b2sub1.ui"), \n',
             '{subst}         actionButton("{prefix}b2sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}         actionButton("{prefix}b2sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}       ) \n',
             '     ), # End of column (6 space) \n',
             '     column( \n',
             '       6, actionButton("{prefix}b2tog0", "Toggle graphics controls"), \n',
             '       conditionalPanel( \n',
             '         condition = "input.{prefix}b2tog0 % 2 == 1", \n',
             '         fluidRow( \n',
             '           column( \n',
             '             6, sliderInput("{prefix}b2siz", "Point size:", \n',
             '                            min = 0, max = 4, value = {ptsiz}, step = 0.25), \n',
             '             radioButtons("{prefix}b2psz", "Plot size:", \n',
             '                          choices = c("Small", "Medium", "Large"), \n',
             '                          selected = "Medium", inline = TRUE), \n',
             '             radioButtons("{prefix}b2fsz", "Font size:", \n',
             '                          choices = c("Small", "Medium", "Large"), \n',
             '                          selected = "Medium", inline = TRUE) \n',
             '           ), \n',
             '           column( \n',
             '             6, radioButtons("{prefix}b2asp", "Aspect ratio:", \n',
             '                             choices = c("Square", "Fixed", "Free"), \n',
             '                             selected = "Square", inline = TRUE), \n',
             '             checkboxInput("{prefix}b2txt", "Show axis text", value = FALSE) \n',
             '           ) \n',
             '         ) \n',
             '       ) \n',
             '     )  # End of column (6 space) \n',
             '   ),   # End of fluidRow (4 space) \n',
             '   fluidRow( \n',
             '     column( \n',
             '       3, style="border-right: 2px solid black", h4("Gene Expression"), \n',
             '       selectInput("{prefix}b2inp1", "Gene 1:", choices=NULL) %>%  \n',
             '         helper(type = "inline", size = "m", fade = TRUE, \n',
             '               title = "Gene expression to colour cells by", \n',
             '               content = c("Select gene to colour cells by gene expression", \n',
             '                          paste0("- Gene expression are coloured in a ", \n',
             '                                 "White-Red colour scheme which can be ", \n',
             '                                 "changed in the plot controls"))), \n',
             '       selectInput("{prefix}b2inp2", "Gene 2:", choices=NULL) %>% \n',
             '         helper(type = "inline", size = "m", fade = TRUE, \n',
             '                title = "Gene expression to colour cells by", \n',
             '                content = c("Select gene to colour cells by gene expression", \n',
             '                            paste0("- Gene expression are coloured in a ", \n',
             '                                   "White-Blue colour scheme which can be ", \n',
             '                                   "changed in the plot controls"))), \n',
             '       actionButton("{prefix}b2tog1", "Toggle plot controls"), \n',
             '       conditionalPanel( \n',
             '         condition = "input.{prefix}b2tog1 % 2 == 1", \n',
             '         radioButtons("{prefix}b2col1", "Colour:", \n',
             '                      choices = c("Red (Gene1); Blue (Gene2)", \n',
             '                                  "Orange (Gene1); Blue (Gene2)", \n',
             '                                  "Red (Gene1); Green (Gene2)", \n',
             '                                  "Green (Gene1); Blue (Gene2)"), \n',
             '                      selected = "Red (Gene1); Blue (Gene2)"), \n',
             '         radioButtons("{prefix}b2ord1", "Plot order:", \n',
             '                      choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
             '                      selected = "Max-1st", inline = TRUE) \n',
             '       ) \n',
             '     ), # End of column (6 space) \n',
             '     column( \n',
             '       6, style="border-right: 2px solid black", \n',
             '       uiOutput("{prefix}b2oup1.ui"), \n',
             '       downloadButton("{prefix}b2oup1.pdf", "Download PDF"), \n',
             '       downloadButton("{prefix}b2oup1.png", "Download PNG"), br(), \n',
             '       div(style="display:inline-block", \n',
             '           numericInput("{prefix}b2oup1.h", "PDF / PNG height:", width = "138px", \n',
             '                        min = 4, max = 20, value = 8, step = 0.5)), \n',
             '       div(style="display:inline-block", \n',
             '           numericInput("{prefix}b2oup1.w", "PDF / PNG width:", width = "138px", \n',
             '                        min = 4, max = 20, value = 10, step = 0.5)) \n',
             '     ), # End of column (6 space) \n',
             '     column( \n',
             '       3, uiOutput("{prefix}b2oup2.ui"), \n',
             '       downloadButton("{prefix}b2oup2.pdf", "Download PDF"), \n',
             '       downloadButton("{prefix}b2oup2.png", "Download PNG"), \n',
             '       br(), h4("Cell numbers"), \n',
             '       dataTableOutput("{prefix}b2.dt") \n',
             '     )  # End of column (6 space) \n',
             '   )    # End of fluidRow (4 space) \n',
             ' ),     # End of tab (2 space) \n',
             ' \n',
             ' ### Tab1.c1: violinplot / boxplot \n',
             ' tabPanel( \n',
             '    HTML("Violinplot / Boxplot"),  \n',
             '   h4("Cell information / gene expression violin plot / box plot"), \n',
             '   "In this tab, users can visualise the gene expression or continuous cell information ",  \n',
             '   "(e.g. Number of UMIs / module score) across groups of cells (e.g. libary / clusters).", \n',
             '   br(),br(), \n',
             '   fluidRow( \n',
             '     column( \n',
             '       3, style="border-right: 2px solid black", \n',
             '       selectInput("{prefix}c1inp1", "Cell information (X-axis):", \n',
             '                   choices = {prefix}conf[grp == TRUE]$UI, \n',
             '                   selected = {prefix}def$grp1) %>%  \n',
             '         helper(type = "inline", size = "m", fade = TRUE, \n',
             '                title = "Cell information to group cells by",  \n',
             '                content = c("Select categorical cell information to group cells by",  \n',
             '                            "- Single cells are grouped by this categorical covariate",  \n',
             '                            "- Plotted as the X-axis of the violin plot / box plot")),  \n',
             '       selectInput("{prefix}c1inp2", "Cell Info / Gene name (Y-axis):", choices=NULL) %>%  \n',
             '         helper(type = "inline", size = "m", fade = TRUE, \n',
             '                title = "Cell Info / Gene to plot", \n',
             '                content = c("Select cell info / gene to plot on Y-axis", \n',
             '                            "- Can be continuous cell information (e.g. nUMIs / scores)", \n',
             '                            "- Can also be gene expression")), \n',
             '       radioButtons("{prefix}c1typ", "Plot type:", \n',
             '                    choices = c("violin", "boxplot"), \n',
             '                    selected = "violin", inline = TRUE), \n',
             '       checkboxInput("{prefix}c1pts", "Show data points", value = FALSE), \n',
             '{subst}       actionButton("{prefix}c1togL", "Toggle to subset cells"), \n',
             '{subst}       conditionalPanel( \n',
             '{subst}         condition = "input.{prefix}c1togL % 2 == 1", \n',
             '{subst}         selectInput("{prefix}c1sub1", "Cell information to subset:", \n',
             '{subst}                     choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                     selected = {prefix}def$grp1), \n',
             '{subst}         uiOutput("{prefix}c1sub1.ui"), \n',
             '{subst}         actionButton("{prefix}c1sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}         actionButton("{prefix}c1sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}       ), br(), br(), \n',
             '       actionButton("{prefix}c1tog", "Toggle graphics controls"), \n',
             '       conditionalPanel( \n',
             '         condition = "input.{prefix}c1tog % 2 == 1", \n',
             '         sliderInput("{prefix}c1siz", "Data point size:",  \n',
             '                     min = 0, max = 4, value = {ptsiz}, step = 0.25),  \n',
             '         radioButtons("{prefix}c1psz", "Plot size:", \n',
             '                      choices = c("Small", "Medium", "Large"), \n',
             '                      selected = "Medium", inline = TRUE), \n',
             '         radioButtons("{prefix}c1fsz", "Font size:", \n',
             '                      choices = c("Small", "Medium", "Large"), \n',
             '                      selected = "Medium", inline = TRUE)) \n',
             '     ), # End of column (6 space) \n',
             '     column(9, uiOutput("{prefix}c1oup.ui"),  \n',
             '            downloadButton("{prefix}c1oup.pdf", "Download PDF"),  \n',
             '            downloadButton("{prefix}c1oup.png", "Download PNG"), br(), \n',
             '            div(style="display:inline-block", \n',
             '                numericInput("{prefix}c1oup.h", "PDF / PNG height:", width = "138px", \n',
             '                             min = 4, max = 20, value = 8, step = 0.5)), \n',
             '            div(style="display:inline-block", \n',
             '                numericInput("{prefix}c1oup.w", "PDF / PNG width:", width = "138px", \n',
             '                             min = 4, max = 20, value = 10, step = 0.5)) \n',
             '     )  # End of column (6 space) \n',
             '   )    # End of fluidRow (4 space) \n',
             ' ),     # End of tab (2 space) \n',
             ' \n',
             '### Tab1.c2: Proportion plot \n',
             'tabPanel( \n',
             '  HTML("Proportion plot"), \n',
             '  h4("Proportion / cell numbers across different cell information"), \n',
             '  "In this tab, users can visualise the composition of single cells based on one discrete ", \n',
             '  "cell information across another discrete cell information. ",  \n',
             '  "Usage examples include the library or cellcycle composition across clusters.", \n',
             '  br(),br(), \n',
             '  fluidRow( \n',
             '    column( \n',
             '      3, style="border-right: 2px solid black", \n',
             '      selectInput("{prefix}c2inp1", "Cell information to plot (X-axis):", \n',
             '                  choices = {prefix}conf[grp == TRUE]$UI, \n',
             '                  selected = {prefix}def$grp2) %>%  \n',
             '        helper(type = "inline", size = "m", fade = TRUE, \n',
             '               title = "Cell information to plot cells by",  \n',
             '               content = c("Select categorical cell information to plot cells by", \n',
             '                           "- Plotted as the X-axis of the proportion plot")), \n',
             '      selectInput("{prefix}c2inp2", "Cell information to group / colour by:", \n',
             '                  choices = {prefix}conf[grp == TRUE]$UI, \n',
             '                  selected = {prefix}def$grp1) %>%  \n',
             '        helper(type = "inline", size = "m", fade = TRUE, \n',
             '               title = "Cell information to group / colour cells by", \n', 
             '               content = c("Select categorical cell information to group / colour cells by", \n',  
             '                           "- Proportion / cell numbers are shown in different colours")), \n',
             '      radioButtons("{prefix}c2typ", "Plot value:", \n',
             '                   choices = c("Proportion", "CellNumbers"), \n',
             '                   selected = "Proportion", inline = TRUE), \n',
             '      checkboxInput("{prefix}c2flp", "Flip X/Y", value = FALSE), \n',
             '{subst}      actionButton("{prefix}c2togL", "Toggle to subset cells"), \n',
             '{subst}      conditionalPanel( \n',
             '{subst}        condition = "input.{prefix}c2togL % 2 == 1", \n',
             '{subst}        selectInput("{prefix}c2sub1", "Cell information to subset:", \n',
             '{subst}                    choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                    selected = {prefix}def$grp1), \n',
             '{subst}        uiOutput("{prefix}c2sub1.ui"), \n',
             '{subst}        actionButton("{prefix}c2sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}        actionButton("{prefix}c2sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}      ), br(), br(), \n',
             '      actionButton("{prefix}c2tog", "Toggle graphics controls"), \n',
             '      conditionalPanel( \n',
             '        condition = "input.{prefix}c2tog % 2 == 1", \n',
             '        radioButtons("{prefix}c2psz", "Plot size:", \n',
             '                     choices = c("Small", "Medium", "Large"), \n',
             '                     selected = "Medium", inline = TRUE), \n',
             '        radioButtons("{prefix}c2fsz", "Font size:", \n',
             '                     choices = c("Small", "Medium", "Large"), \n',
             '                     selected = "Medium", inline = TRUE)) \n',
             '    ), # End of column (6 space) \n',
             '    column(9, uiOutput("{prefix}c2oup.ui"),  \n',
             '           downloadButton("{prefix}c2oup.pdf", "Download PDF"),  \n',
             '           downloadButton("{prefix}c2oup.png", "Download PNG"), br(), \n',
             '           div(style="display:inline-block", \n',
             '               numericInput("{prefix}c2oup.h", "PDF / PNG height:", width = "138px", \n',
             '                            min = 4, max = 20, value = 8, step = 0.5)), \n',
             '           div(style="display:inline-block", \n',
             '               numericInput("{prefix}c2oup.w", "PDF / PNG width:", width = "138px", \n',
             '                            min = 4, max = 20, value = 10, step = 0.5)) \n',
             '    )  # End of column (6 space) \n',
             '  )    # End of fluidRow (4 space) \n',
             '),     # End of tab (2 space) \n',
             ' \n',             
             '  ### Tab1.d1: Multiple gene expr \n',
             '  tabPanel( \n',
             '    HTML("Bubbleplot / Heatmap"), \n',
             '    h4("Gene expression bubbleplot / heatmap"), \n',
             '    "In this tab, users can visualise the gene expression patterns of ", \n',
             '    "multiple genes grouped by categorical cell information (e.g. library / cluster).", br(), \n',
             '    "The normalised expression are averaged, log-transformed and then plotted.", \n',
             '    br(),br(), \n',
             '    fluidRow( \n',
             '      column( \n',
             '        3, style="border-right: 2px solid black", \n',
             '        textAreaInput("{prefix}d1inp", HTML("List of gene names <br /> \n',
             '                                          (Max 50 genes, separated <br /> \n',
             '                                           by , or ; or newline):"), \n',
             '                      height = "200px", \n',
             '                      value = paste0({prefix}def$genes, collapse = ", ")) %>% \n',
             '          helper(type = "inline", size = "m", fade = TRUE, \n',
			 #deletion from #75
             #'                 title = "List of genes to plot on bubbleplot / heatmap", \n',
			 #end deletion
			 #insert from #75 
			 '					title = "List of genes to plot on bubbleplot / heatmap / stacked plot", \n',
			 #end insert #75
             '                 content = c("Input genes to plot", \n',
             '                             "- Maximum 50 genes (due to ploting space limitations)", \n',
             '                             "- Genes should be separated by comma, semicolon or newline")), \n',
             '        selectInput("{prefix}d1grp", "Group by:", \n',
             '                    choices = {prefix}conf[grp == TRUE]$UI, \n',
             '                    selected = {prefix}conf[grp == TRUE]$UI[1]) %>% \n',
             '          helper(type = "inline", size = "m", fade = TRUE, \n',
             '                 title = "Cell information to group cells by", \n',
             '                 content = c("Select categorical cell information to group cells by", \n',
             '                             "- Single cells are grouped by this categorical covariate", \n',
			 #Deletion from #75
             #'                             "- Plotted as the X-axis of the bubbleplot / heatmap")), \n',
             #'        radioButtons("{prefix}d1plt", "Plot type:", \n',
             #'                     choices = c("Bubbleplot", "Heatmap"), \n',
             #'                     selected = "Bubbleplot", inline = TRUE), \n',
			 #end deletion from #75
			 
			 #insert from #75 line 2002
			 '                             "- Plotted as the X-axis of the bubbleplot / heatmap / stacked plot")), \n',
             '        radioButtons("sc1d1plt", "Plot type:",  \n',
             '                     choices = c("Bubbleplot", "Heatmap", "Stacked Violin", "Stacked Boxplot"),  \n',
             '                     selected = "Bubbleplot", inline = FALSE) %>%  \n',
             '          helper(type = "inline", size = "m", fade = TRUE,  \n',
             '                 title = "Different types of plot",  \n',
             '                 content = c("The 4 plot options could be devided into 2 types",  \n',
             '                             "- Bubbleplot / Heatmap are based group summmarization and support scaling and clustering",  \n',
             '                             "- Stacked plots are to visualise group distribution and NOT support scaling and clustering")),  \n',
			 #end insert from #75 line 2011
             '        radioButtons("{prefix}d1scl", "Scale gene expression", 	choices=c("Expression","Z-score","Fold change"), selected = "Expression", inline=TRUE), \n',
             '        checkboxInput("{prefix}d1row", "Cluster rows (genes)", value = TRUE), \n',
             '        checkboxInput("{prefix}d1col", "Cluster columns (samples)", value = FALSE), \n',
             '        br(), \n',
             '{subst}        actionButton("{prefix}d1togL", "Toggle to subset cells"), \n',
             '{subst}        conditionalPanel( \n',
             '{subst}          condition = "input.{prefix}d1togL % 2 == 1", \n',
             '{subst}          selectInput("{prefix}d1sub1", "Cell information to subset:", \n',
             '{subst}                      choices = {prefix}conf[grp == TRUE]$UI, \n',
             '{subst}                      selected = {prefix}def$grp1), \n',
             '{subst}          uiOutput("{prefix}d1sub1.ui"), \n',
             '{subst}          actionButton("{prefix}d1sub1all", "Select all groups", class = "btn btn-primary"), \n',
             '{subst}          actionButton("{prefix}d1sub1non", "Deselect all groups", class = "btn btn-primary") \n',
             '{subst}        ), br(), br(), \n',
             '        actionButton("{prefix}d1tog", "Toggle graphics controls"), \n',
             '        conditionalPanel( \n',
             '          condition = "input.{prefix}d1tog % 2 == 1", \n',
             '          radioButtons("{prefix}d1cols", "Colour scheme:", \n',
             '                       choices = c("White-Red", "Blue-Yellow-Red", \n',
             '                                   "Yellow-Green-Purple"), \n',
             '                       selected = "Blue-Yellow-Red"), \n',
             '          radioButtons("{prefix}d1psz", "Plot size:", \n',
             '                       choices = c("Small", "Medium", "Large"), \n',
             '                       selected = "Medium", inline = TRUE), \n',
             '          radioButtons("{prefix}d1fsz", "Font size:", \n',
             '                       choices = c("Small", "Medium", "Large"), \n',
             '                       selected = "Medium", inline = TRUE)) \n',
             '      ), # End of column (6 space) \n',
             '      column(9, h4(htmlOutput("{prefix}d1oupTxt")), \n',
             '             uiOutput("{prefix}d1oup.ui"), \n',
             '             downloadButton("{prefix}d1oup.pdf", "Download PDF"), \n',
             '             downloadButton("{prefix}d1oup.png", "Download PNG"), br(), \n',
             '             div(style="display:inline-block", \n',
             '                 numericInput("{prefix}d1oup.h", "PDF / PNG height:", width = "138px", \n',
             '                              min = 4, max = 20, value = 10, step = 0.5)), \n',
             '             div(style="display:inline-block", \n',
             '                 numericInput("{prefix}d1oup.w", "PDF / PNG width:", width = "138px", \n',
             '                              min = 4, max = 20, value = 10, step = 0.5)) \n',
             '      )  # End of column (6 space) \n',
             '    )    # End of fluidRow (4 space) \n',
             '  ),      # End of tab (2 space) \n',
			 
			 '#INSERT DAVE New tab panel\n',
			 ### Dave added Tab1.d2
			'	### Tab1.d2: Single gene expr \n',

			
    
			'	tabPanel( \n',
			'	    HTML("Single Gene analysis"), \n',
			'	h4("Single gene expression bubbleplot / heatmap"), \n',
			'	"In this tab, users can visualise the gene expression patterns of a", \n',
			'	"SINGLE gene grouped by categorical cell information (e.g. library / cluster).", br(), \n',
			'	"The normalised expression are averaged, log-transformed and then plotted.", \n',
			'	    br(),br(), \n',
			'	    fluidRow( \n',
			'	      column( \n',
			'	         3, style="border-right: 2px solid black",  \n\n\n',
		 
		 
			'		 selectInput("{prefix}d2inp", "Gene name:", choices=NULL) %>%   \n',
			'			   helper(type = "inline", size = "m", fade = TRUE,  \n',
			'			          title = "Gene expression to colour cells by",  \n',
			'			          content = c("Select gene to colour cells by gene expression",  \n',
			'			                      paste0("- Gene expression are coloured in a ",  \n',
			'			                             "White-Red colour scheme which can be ", \n', 
			'			                             "changed in the plot controls"))) , \n',
					 
							 
			'	        selectInput("{prefix}d2grp", "Group by:", \n',
			'	                    choices = {prefix}conf[grp == TRUE]$UI, \n',
			'	                    selected = {prefix}conf[grp == TRUE]$UI[1]) %>% \n',
			'	          helper(type = "inline", size = "m", fade = TRUE, \n',
			'	                 title = "Cell information to group cells by", \n',
			'	                 content = c("Select categorical cell information to group cells by", \n',
			'	                             "- Single cells are grouped by this categorical covariate", \n',
			'	                             "- Plotted as the X-axis of the bubbleplot / heatmap")), \n\n\n',
		 
		 
			'			 selectInput("{prefix}d2split", "Split by:", \n',
			'			             choices = {prefix}conf[grp == TRUE]$UI, \n',
			'			             selected = {prefix}conf[grp == TRUE]$UI[1]) %>%  \n',
			'			   helper(type = "inline", size = "m", fade = TRUE, \n',
			'			          title = "Cell information to split cells by", \n',
			'			          content = c("Select categorical cell information to split cells by", \n',
			'			                      "- Single cells are grouped by this categorical covariate", \n',
			'			                      "- Plotted as the X-axis of the bubbleplot / heatmap")), \n\n\n',
		 
		 
			'	        radioButtons("{prefix}d2plt", "Plot type:", \n',
			'	                     choices = c("Bubbleplot", "Heatmap"), \n',
			'	                     selected = "Bubbleplot", inline = TRUE), \n',
			'	        radioButtons("{prefix}d2scl", "Scale gene expression",	choices=c("Expression","Z-score","Fold change"), selected = "Expression", inline=TRUE), \n',
			'	        checkboxInput("{prefix}d2row", "Cluster rows (genes)", value = TRUE), \n',
			'	        checkboxInput("{prefix}d2col", "Cluster columns (samples)", value = FALSE), \n',
			'	        br(), \n',
			'	        actionButton("{prefix}d2togL", "Toggle to subset cells"), \n',
			'	        conditionalPanel( \n',
			'	          condition = "input.{prefix}d2togL % 2 == 1", \n',
			'	          selectInput("{prefix}d2sub1", "Cell information to subset:", \n',
			'	                      choices = {prefix}conf[grp == TRUE]$UI, \n',
			'	                      selected = {prefix}def$grp1), \n',
			'	           uiOutput("{prefix}d2sub1.ui"),  \n',
			'	          actionButton("{prefix}d2sub1all", "Select all groups", class = "btn btn-primary"), \n',
			'	          actionButton("{prefix}d2sub1non", "Deselect all groups", class = "btn btn-primary") \n',
			'	        ), br(), br(), \n\n\n',
        

			'	        actionButton("{prefix}d2tog", "Toggle graphics controls"), \n',
			'	        conditionalPanel( \n',
			'	          condition = "input.{prefix}d2tog % 2 == 1", \n',
			'	          radioButtons("{prefix}d2cols", "Colour scheme:", \n',
			'	                       choices = c("White-Red", "Blue-Yellow-Red", \n',
			'	                                   "Yellow-Green-Purple"), \n',
			'	                       selected = "Blue-Yellow-Red"), \n',
			'	          radioButtons("{prefix}d2psz", "Plot size:", \n',
			'	                       choices = c("Small", "Medium", "Large"), \n',
			'	                       selected = "Medium", inline = TRUE), \n',
			'	          radioButtons("{prefix}d2fsz", "Font size:", \n',
			'	                       choices = c("Small", "Medium", "Large"), \n',
			'	                       selected = "Medium", inline = TRUE)) \n',
			'	      ), # End of column (6 space) \n',
			'	      column(9, h4(htmlOutput("{prefix}d2oupTxt")), \n',
			'	             uiOutput("{prefix}d2oup.ui"), \n',
			'	             downloadButton("{prefix}d2oup.pdf", "Download PDF"), \n',
			'	             downloadButton("{prefix}d2oup.png", "Download PNG"), br(), \n',
			'	             div(style="display:inline-block", \n',
			'	                 numericInput("{prefix}d2oup.h", "PDF / PNG height:", width = "138px", \n',
			'	                              min = 4, max = 20, value = 10, step = 0.5)), \n',
			'	             div(style="display:inline-block", \n',
			'	                 numericInput("{prefix}d2oup.w", "PDF / PNG width:", width = "138px", \n',
			'	                              min = 4, max = 20, value = 10, step = 0.5)) \n',
			'	      )  # End of column (6 space)  \n',
			'	    )    # End of fluidRow (4 space) \n',
			'	   )     # End of tab (2 space) \n\n',

			 
			'				 # end INSERT DAVE new tab panel \n',
	 # end INSERT DAVE new tab panel 			 
             '   \n')
}

#' Write code for final portion of ui.R
#'
#' @param footnote shiny app footnote
#' 
#' @rdname wrUIend
#' @export wrUIend
#'
wrUIend <- function(footnote) {
  if(is.list(footnote)){
    f1 = ''; f2 = ''; f3 = ''; f4 = ''; f5 = ''; f6 = ''; f7 = ''; f8 = ''
    if(!is.null(footnote$author)){ f1 = paste0('"',footnote$author,' ",')}
    if(!is.null(footnote$title)){  f2 = paste0('"',footnote$title,' ",')}
    if(!is.null(footnote$journal)){f3 = paste0('em("',footnote$journal,' "),')}
    if(!is.null(footnote$volume)){ f4 = paste0('strong("',footnote$volume,', "),')}
    if(!is.null(footnote$page)){   f5 = paste0('"',footnote$page,' ",')}
    if(!is.null(footnote$year)){   f6 = paste0('"(',footnote$year,') ",')}
    if(!is.null(footnote$doi)){    f7 = paste0('"doi: ',footnote$doi,' ",')}
    if(!is.null(footnote$link)){   f8 = paste0('a("[Link]", href = "',footnote$link,'", target="_blank"),')}
    f0 = paste0('strong("Reference: "),', f1, f2, f3, f4, f5, f6, f7, f8, 
                'style = "font-size: 125%;"')
  } else {
    f0 = paste0('"', footnote[[1]], '", style = "font-size: 125%;"')
  }
  
  glue::glue('   \n',
             '   \n',
             'br(), \n',
             'p({f0}), \n',
             'p(em("This webpage was made using "), a("ShinyCell", \n', 
             '  href = "https://github.com/SGDDNB/ShinyCell",target="_blank")), \n',
             'br(),br(),br(),br(),br() \n',
             '))) \n',
             ' \n',
             ' \n',
             ' \n',
             ' \n')
}

#' Write code for google-analytics.html
#'
#' @param gaID Google analytics tracking ID (e.g. "UA-123456789-0")
#' 
#' @rdname wrUIga
#' @export wrUIga
#'
wrUIga <- function(gaID) {
  glue::glue('<!-- Global site tag (gtag.js) - Google Analytics --> \n',
             '  <script async src="https://www.googletagmanager.com/gtag/js?id={gaID}"></script> \n',
             '  <script> \n',
             '  window.dataLayer = window.dataLayer || []; \n',
             'function gtag(){{dataLayer.push(arguments);}} \n',
             'gtag(\'js\', new Date()); \n',
             ' \n',
             'gtag(\'config\', \'{gaID}\'); \n',
             '</script> \n')
}

#end writer.R