chore: cascade dev → gsource (expression_matrix_class deprecation + overlap ids flip)

DESCRIPTION

@@ -24,7 +24,6 @@ Description: Definitions for the Giotto object and its subobjects.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Depends:
     R (>= 4.5.0)
 Imports:
@@ -161,3 +160,4 @@ URL: https://giotto-suite.github.io/GiottoClass/
 biocViews: Software, Technology, Spatial
 VignetteBuilder: knitr
 BugReports: https://github.com/giotto-suite/Giotto/issues
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -413,6 +413,7 @@ exportMethods(settleGeom)
 exportMethods(shear)
 exportMethods(snap)
 exportMethods(spatIDs)
+exportMethods(spatRelate)
 exportMethods(spatShift)
 exportMethods(spatUnit)
 exportMethods(spin)

R/classes-overlaps.R

@@ -21,11 +21,10 @@ setClass("overlapIntensity", contains = c("overlapInfo", "VIRTUAL"))
 #' @title Polygon and Point Relationships
 #' @description
 #' Utility class for storing overlaps relationships between polygons and points
-#' in a sparse `data.table` format. Retrieve the unique ID index of overlapped
-#' points `[i, ]`. Get indices of which polys are overlapping specific feature
-#' species using `[, j]`.
-#'
-#' Subsetting with `ids = FALSE` and `[i, j]` indexing is also supported.
+#' in a sparse `data.table` format. `[i, ]` / `[, j]` / `[i, j]` all return a
+#' subset `overlapPointDT`. To retrieve indices instead — feat_ID_uniqs
+#' overlapped by poly i, or poly indices overlapping feature j — pass
+#' `ids = TRUE`.
 #'
 #' Supports `as.matrix` for conversion to `dgCMatrix`. Contained poly and
 #' feature names simplify rownames/colnames and empty row/col creation.
@@ -49,14 +48,15 @@ setClass("overlapIntensity", contains = c("overlapInfo", "VIRTUAL"))
 #' polygons
 #' @param j numeric, character, logical. Index of or name of feature being
 #' overlapped.
-#' @param use_names logical (default = `FALSE`). Whether to return as integer
-#' indices or with character ids.
-#' @param ids logical (default = `TRUE`). Whether to return the requested
-#' integer indices (`TRUE`) or the subset overlap object (`FALSE`).
+#' @param use_names logical (default = `FALSE`). When `ids = TRUE`, whether
+#' to return integer indices (`FALSE`) or character ids (`TRUE`).
+#' @param ids logical (default = `FALSE`). Whether to return the requested
+#' integer indices (`TRUE`) or the subset overlap object (`FALSE`, default).
 #' @param drop not used.
 #' @param \dots additional params to pass (none implemented)
-#' @returns integer or character if only `i` or `j` provided, depending on
-#' `use_names`. A subset `overlapPointDT` if both `i` and `j` are used.
+#' @returns A subset `overlapPointDT` by default. When `ids = TRUE`,
+#' an integer (or character via `use_names = TRUE`) vector of the queried
+#' indices.
 #' @examples
 #' g <- GiottoData::loadGiottoMini("vizgen")
 #' poly <- g[["spatial_info", "z0"]][[1]]
@@ -68,19 +68,19 @@ setClass("overlapIntensity", contains = c("overlapInfo", "VIRTUAL"))
 #' dim(ovlp)
 #' nrow(ovlp) # number of relationships
 #'
-#' # get feature unique IDs overlapped by nth poly
-#' ovlp[1] # check one (no overlaps returns integer(0))
-#' ovlp[1:5] # check multiple
-#' ovlp[1:5, use_names = TRUE] # returns feature names, but no longer unique
+#' # subset (default) — returns an overlapPointDT
+#' ovlp[1:10] # first 10 polys
+#' ovlp[, 1:10] # first 10 feature species
+#' ovlp[1:10, 1:10] # both
 #'
-#' # get integer index of poly(s) overlapping particular feature species
-#' ovlp[, 1]
-#' ovlp[, "Mlc1"] # this is the same
+#' # selection query — feature unique IDs overlapped by nth poly
+#' ovlp[1, ids = TRUE] # integer feat_ID_uniqs (integer(0) if no overlap)
+#' ovlp[1:5, ids = TRUE]
+#' ovlp[1:5, ids = TRUE, use_names = TRUE] # feature names instead of ints
 #'
-#' # get a subset of overlap object
-#' ovlp[1:10, ids = FALSE] # subset to first 10 polys
-#' ovlp[, 1:10, ids = FALSE] # subset to first 10 feature species
-#' ovlp[1:10, 1:10] # subset to first 10 polys and first 10 features species
+#' # selection query — poly indices overlapping particular feature species
+#' ovlp[, 1, ids = TRUE]
+#' ovlp[, "Mlc1", ids = TRUE]
 #' @exportClass overlapPointDT
 setClass("overlapPointDT",
     contains = "overlapPoint",

R/create.R

@@ -74,15 +74,14 @@ NULL
 #' from \code{\link{createGiottoInstructions}}
 #' @param cores how many cores or threads to use to read data if paths are
 #' provided
-#' @param expression_matrix_class class of expression matrix to
-#' use (e.g. 'dgCMatrix', 'DelayedArray')
+#' @param expression_matrix_class deprecated. See `?createExprObj` for details
 #' @param backend backend to use (optional). One of:
-#' 
+#'
 #'   * `NULL` - (default) in memory object
 #'   * `filepath` - path at which to set up a project directory. Does not have
 #'     to already exist. Sets the backend manager as `gDirSource` by default.
 #'   * `gsource`-inheriting - A specific backend manager to use
-#' 
+#'
 #'   `filepath` and `gsource` both require {GiottoDisk}.
 #' @param h5_file deprecated. Use `backend` instead
 #' @param verbose be verbose when building Giotto object
@@ -226,7 +225,7 @@ createGiottoObject <- function(expression,
     instructions = NULL,
     cores = determine_cores(),
     raw_exprs = NULL,
-    expression_matrix_class = c("dgCMatrix", "DelayedArray"),
+    expression_matrix_class = deprecated(),
     backend = NULL,
     h5_file = deprecated(),
     verbose = FALSE) {
@@ -245,6 +244,13 @@ createGiottoObject <- function(expression,
         images <- c(images, largeImages)
     }
 
+    if (is_present(expression_matrix_class)) {
+        warning(sprintf(
+            "[createGiottoObject] param '%s' is deprecated",
+            "expression_matrix_class"),
+        call. = FALSE)
+    }
+
     if (is_present(h5_file)) backend <- h5_file
     if (!is_present(h5_file)) h5_file <- NULL
     if (!is.null(backend)) {
@@ -363,8 +369,7 @@ createGiottoObject <- function(expression,
             sparse = TRUE,
             cores = cores,
             default_feat_type = expression_feat,
-            verbose = debug_msg,
-            expression_matrix_class = expression_matrix_class
+            verbose = debug_msg
         )
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
         gobject <- setExpression(

R/data_evaluation.R

@@ -78,9 +78,6 @@ evaluate_input <- function(type, x, ...) {
 #' @param inputmatrix inputmatrix to evaluate
 #' @param sparse create sparse matrix (default = TRUE)
 #' @param cores how many cores to use
-#' @param expression_matrix_class `character` (optional). Matrix
-#'   representation to convert to. If left as NULL, no conversions will
-#'   be attempted
 #' @details The inputmatrix can be a matrix, sparse matrix, data.frame,
 #' data.table or path to any of these.
 #' @keywords internal

R/data_input.R

@@ -33,8 +33,8 @@ readExprMatrix <- function(
     checkmate::assert_flag(transpose)
     if (is_present(expression_matrix_class)) {
         warning(sprintf(
-            "[readExprMatrix] param '%s' is deprecated", 
-            "expression_matrix_class"), 
+            "[readExprMatrix] param '%s' is deprecated",
+            "expression_matrix_class"),
         call. = FALSE)
     }
 

R/generics.R

@@ -195,6 +195,13 @@ setGeneric("splitGeom", function(x, ...) standardGeneric("splitGeom"))
 setGeneric("overlaps", function(x, ...) standardGeneric("overlaps"))
 
 
+# Methods and documentations found in methods-relate.R
+setGeneric(
+    "spatRelate",
+    function(x, y, relation = "intersects", ...) standardGeneric("spatRelate")
+)
+
+
 
 # Giotto subnesting ####
 # All methods and documentations found in methods-nesting.R

R/methods-extract.R

@@ -662,8 +662,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,coordDataDT,missing,missing,
-#' ANY-method [<-,coordDataDT,missing,missing-method
+#' @aliases [<-,coordDataDT,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{coordinates} slot in giotto S4
@@ -742,8 +741,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,metaData,missing,missing,
-#' ANY-method [<-,metaData,missing,missing-method
+#' @aliases [<-,metaData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{metaDT} slot in giotto S4
@@ -783,8 +781,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,dimObj,missing,missing,
-#' ANY-method [<-,dimObj,missing,missing-method
+#' @aliases [<-,dimObj,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{coordinates} slot in giotto S4 dimObj
@@ -844,8 +841,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,exprData,missing,missing,
-#' ANY-method [<-,exprData,missing,missing-method
+#' @aliases [<-,exprData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{exprMat} slot in giotto S4
@@ -876,8 +872,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,spatNetData,missing,missing,
-#' ANY-method [<-,spatNetData,missing,missing-method
+#' @aliases [<-,spatNetData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{network} slot in giotto S4
@@ -906,8 +901,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,nnData,missing,missing,
-#' ANY-method [<-,nnData,missing,missing-method
+#' @aliases [<-,nnData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{network} slot in giotto S4
@@ -968,8 +962,7 @@ setMethod(
 
 
 #' @rdname replace_bracket
-#' @aliases [<-,enrData,missing,missing,
-#' ANY-method [<-,enrData,missing,missing-method
+#' @aliases [<-,enrData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{enrichDT} slot in giotto S4
@@ -1000,8 +993,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,spatGridData,missing,missing,
-#' ANY-method [<-,spatGridData,missing,missing-method
+#' @aliases [<-,spatGridData,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{gridDT} slot in giotto S4
@@ -1083,8 +1075,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,giottoPoints,missing,missing,
-#' ANY-method [<-,giottoPoints,missing,missing-method
+#' @aliases [<-,giottoPoints,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{spatVector} slot in giotto S4
@@ -1163,7 +1154,7 @@ setMethod(
             if (!inherits(o[[feat]], "overlapInfo")) {
                 warning("[subset overlaps feats] unrecognized overlap type")
             }
-            o[[feat]] <- o[[feat]][, i, ids = FALSE]
+            o[[feat]] <- o[[feat]][, i]
         }
         o
     }
@@ -1200,7 +1191,7 @@ setMethod(
             }
             next
         }
-        x@overlaps[[feat]] <- x@overlaps[[feat]][i, ids = FALSE]
+        x@overlaps[[feat]] <- x@overlaps[[feat]][i]
     }
     x
 }
@@ -1389,8 +1380,7 @@ setMethod(
 
 
 #' @rdname replace_bracket
-#' @aliases [<-,giottoPolygon,missing,missing,
-#' ANY-method [<-,giottoPolygon,missing,missing-method
+#' @aliases [<-,giottoPolygon,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{spatVector} slot in giottoPolygon
@@ -1417,12 +1407,11 @@ setMethod("[",
         i = "gIndex",
         j = "missing",
         drop = "missing"
-    ), function(x, i, j, ..., use_names = FALSE, ids = TRUE, drop) {
-        if (!isTRUE(ids)) {
-            res <- .subset_overlap_point_dt_i(x, i)
-            return(res)
+    ), function(x, i, j, ..., use_names = FALSE, ids = FALSE, drop) {
+        if (isTRUE(ids)) {
+            return(.select_overlap_point_dt_i(x, i, use_names = use_names))
         }
-        .select_overlap_point_dt_i(x, i, use_names = use_names)
+        .subset_overlap_point_dt_i(x, i)
     }
 )
 
@@ -1434,12 +1423,11 @@ setMethod("[",
         i = "missing",
         j = "gIndex",
         drop = "missing"
-    ), function(x, i, j, ..., use_names = FALSE, ids = TRUE, drop) {
-        if (!isTRUE(ids)) {
-            res <- .subset_overlap_point_dt_j(x, j)
-            return(res)
+    ), function(x, i, j, ..., use_names = FALSE, ids = FALSE, drop) {
+        if (isTRUE(ids)) {
+            return(.select_overlap_point_dt_j(x, j, use_names = use_names))
         }
-        .select_overlap_point_dt_j(x, j, use_names = use_names)
+        .subset_overlap_point_dt_j(x, j)
     }
 )
 
@@ -1614,8 +1602,7 @@ setMethod(
 )
 
 #' @rdname replace_bracket
-#' @aliases [<-,affine2d,missing,missing,
-#' ANY-method [<-,affine2d,missing,missing-method
+#' @aliases [<-,affine2d,missing,missing-method
 #' @docType methods
 #' @section \code{`[<-`} methods:
 #'   Assign to \code{affine} slot in affine2d