Numerous changes to the core workflow, now all

paths go through splicejamFigure(), including
the R-shiny app. Fixed all internal warnings,
added visual testthat tests, added test
environment. Import supports bigwig, bigbed,
bed, and SJ.out.tab from STAR. Intermediate
data.frame keeps all coverage coordinates
in NumericList and not per-row tidy format,
speed and memory improvements. Updated pkgdown
docs. Recategorized all functions.

Author: jmw86069

.Rbuildignore

@@ -8,3 +8,7 @@
 ^doc$
 ^Meta$
 ^data-raw$
+^.vscode
+^.vdoc.*
+^TODO_.*md$
+^gencode.*$

.gitignore

@@ -1,10 +1,27 @@
-inst/doc
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
-*_memoise
-gencode*
-doc
-Meta
-.vscode
+.Rproj.user/
+.Rhistory
+.Rapp.history
+.RData
+.RDataTmp
+.Ruserdata
+*-Ex.R
+/*.tar.gz
+/*.Rcheck/
+/doc/
+/Meta/
+inst/doc
+vignettes/*.html
+vignettes/*.pdf
+.httr-oauth
+/cache
+*_cache/
+rsconnect/
+.vscode
+air.toml
+.vdoc*
+/.quarto/
+**/*.quarto_ipynb
+*_memoise
+gencode*annotation*
+TODO_*
+/docs/*/*.md

DESCRIPTION

@@ -20,8 +20,8 @@ Description: Jam Bioinformatics methods for RNA-seq and other genomics
     methods for manipulating gene expression data.
 Depends: R (>= 3.5.0)
 biocViews:
-Imports: jamba(>= 1.0.0),
-    jamma(>= 0.0.38.900),
+Imports: jamba(>= 1.0.4),
+    jamma(>= 0.0.40.900),
     colorjam(>= 0.0.35.900),
     data.table,
     GenomicRanges,
@@ -44,7 +44,6 @@ Imports: jamba(>= 1.0.0),
     shinyjqui,
     shinycssloaders,
     shinyjs,
-    cowplot,
     plotly,
     DT,
     caTools,
@@ -64,6 +63,7 @@ Suggests:
     org.Mm.eg.db,
     farrisdata(>= 0.0.9.900),
     testthat(>= 3.0.0),
+    cowplot,
     vdiffr
 License: GPL-2
 Encoding: UTF-8
@@ -76,9 +76,9 @@ Remotes:
     github::RinteRface/shinydashboardPlus,
     github::Yang-Tang/shinyjqui,
     github::rnabioco/cpp11bigwig
-URL: http://github.com/jmw86069/splicejam
-BugReports: http://github.com/jmw86069/splicejam/issues
+URL: https://jmw86069.github.io/splicejam
+BugReports: https://github.com/jmw86069/splicejam/issues
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.0.0.9000
 Config/testthat/edition: 3

NAMESPACE

@@ -35,7 +35,6 @@ export(getGRLgaps)
 export(getGRcoverageFromBw)
 export(getGRgaps)
 export(getGtfAttrs)
-export(get_fn_envir)
 export(grl2df)
 export(groups2contrasts)
 export(import_juncs_from_bed)

NEWS.md

@@ -1,10 +1,29 @@
 # splicejam 0.0.91.900
 
+* Re-categorized all function families, for "See Also"
+and for pkgdown site docs.
+* Updated pkgdown site help docs.
 * Added 'testthat', 'vdiffr' with `splicejamFigure()`.
 * Added data `'sjenvtest'` with two genes from Farris et al.
+* Simplified vignette 'create-a-sashimi-plot.Rmd'.
+* Removed all other vignettes, no longer necessary.
+* Updated 'README.Rmd' with the abbreviated workflow,
+added alt text.
+
 
 ## Changes
 
+* `splicejamFigure()`
+
+   * returns 'timings_df' `data.frame` with time duration
+   for each of several steps in the process.
+   * Now adds 10% to y-axis ranges to accomodate junction labels.
+
+* `plotSashimi()` now positions junction labels below the arc
+for negative strand genes, junctions with negative scores.
+* `import_juncs_from_bed()` help docs include formatting for
+BED, bigBed using optional 'name' column to store scores
+higher than 1000, or 'SJ.out.tab' as produced by STAR aligner.
 * `sashimiDataConstants()`
 
    * Now properly defines 'color_sub' when farrisdata is used.
@@ -16,6 +35,12 @@
 
 * `sashimiAppServer()` no longer assumes 'exonsByTx' exists,
 will skip this step if not present.
+* `exoncov2polygons()`
+
+   * Refactored to use `NumericList` coverage data as-is without
+   further processing.
+   * Updated StatUnpackPolygon to handle this format, adding
+   initial and final point with y-value 0.
 
 # splicejam 0.0.90.900
 

R/data-sjenvtest.R

@@ -1,29 +1,29 @@
-
-#' Splicejam Environment Test Data
-#' 
-#' Splicejam Environment Test Data, minimal subset of
-#' Farris et al bulk RNA-seq data from mouse hippocampus.
-#' It contains only 'CellType' values CA1 and CA2, with
-#' both 'Compartment' values CB (cell body) and
-#' DE (dendrites).
-#' 
-#' @family splicejam data
-#' 
-#' @format `environment` with components suitable as
-#'    input to `splicejamFigure()` and other functions
-#'    which accept environment as input, typically
-#'    using argument 'sjenv'.
-#' \describe{
-#'   \item{tx2geneDF}{`data.frame` with colnames including
-#'     the minimum required: 'gene_name', 'transcript_id'.}
-#'   \item{detectedGenes}{`character` vector of gene symbols.}
-#'   \item{detectedTx}{`character` vector of 'transcript_id'.}
-#'   \item{flatExonsByGene}{`GRangesList` named by 'gene_name'}
-#'   \item{flatExonsByTx}{`GRangesList` named by 'transcript_id'}
-#'   \item{txdb}{`TxDb` object used to create various exon
-#'     `GRanges` and `GRangesList` intermediate objects.
-#'     Not essential for processing, but often useful.}
-#'   \item{filesDF}{`data.frame` with colnames including
-#'     the minimum required: 'sample_id', 'url', 'type'}
-#' }
-"sjenvtest"
+
+#' Splicejam Environment Test Data
+#' 
+#' Splicejam Environment Test Data, minimal subset of
+#' Farris et al bulk RNA-seq data from mouse hippocampus.
+#' It contains only 'CellType' values CA1 and CA2, with
+#' both 'Compartment' values CB (cell body) and
+#' DE (dendrites).
+#' 
+#' @family Splicejam data
+#' 
+#' @format `environment` with components suitable as
+#'    input to `splicejamFigure()` and other functions
+#'    which accept environment as input, typically
+#'    using argument 'sjenv'.
+#' \describe{
+#'   \item{tx2geneDF}{`data.frame` with colnames including
+#'     the minimum required: 'gene_name', 'transcript_id'.}
+#'   \item{detectedGenes}{`character` vector of gene symbols.}
+#'   \item{detectedTx}{`character` vector of 'transcript_id'.}
+#'   \item{flatExonsByGene}{`GRangesList` named by 'gene_name'}
+#'   \item{flatExonsByTx}{`GRangesList` named by 'transcript_id'}
+#'   \item{txdb}{`TxDb` object used to create various exon
+#'     `GRanges` and `GRangesList` intermediate objects.
+#'     Not essential for processing, but often useful.}
+#'   \item{filesDF}{`data.frame` with colnames including
+#'     the minimum required: 'sample_id', 'url', 'type'}
+#' }
+"sjenvtest"

R/jam-sets.R

@@ -25,7 +25,7 @@
 #'    updated to reflect the count of each element.
 #' @param verbose logical indicating whether to print verbose output.
 #'
-#' @family jam list functions
+#' @family Internal utility functions
 #'
 #' @examples
 #' set.seed(123);

R/jambio-data.R

@@ -17,7 +17,7 @@
 #'    begins at position 100, the junction would end at position
 #'    99.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' # The code below is used to create the junction test data
@@ -38,7 +38,8 @@
 #'
 #' # To plot junctions, use grl2df(..., shape="junction")
 #' junc_df <- grl2df(test_junc_gr, shape="junction")
-#' gg1 <- ggplot(junc_df, aes(x=x, y=y, group=id, fill=gr_name)) +
+#' gg1 <- ggplot2::ggplot(junc_df,
+#'    ggplot2::aes(x=x, y=y, group=id, fill=gr_name)) +
 #'    ggforce::geom_diagonal_wide(alpha=0.7) +
 #'    colorjam::theme_jam() +
 #'    colorjam::scale_fill_jam()
@@ -69,7 +70,7 @@
 #'    begins at position 100, the junction would end at position
 #'    99.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' # The code below is used to create the junction test data
@@ -88,12 +89,13 @@
 #'
 #' # To plot junctions, use grl2df(..., shape="junction")
 #' junc_wide_df <-grl2df(test_junc_wide_gr, shape="junction")
-#' ggWide1 <- ggplot(junc_wide_df, aes(x=x, y=y, group=id, fill=gr_name)) +
+#' ggWide1 <- ggplot2::ggplot(junc_wide_df,
+#'    ggplot2::aes(x=x, y=y, group=id, fill=gr_name)) +
 #'    ggforce::geom_diagonal_wide(alpha=0.7) +
 #'    colorjam::theme_jam() +
 #'    colorjam::scale_fill_jam() +
-#'    xlab("chr1") +
-#'    ggtitle("junctions (full intron width)")
+#'    ggplot2::xlab("chr1") +
+#'    ggplot2::ggtitle("junctions (full intron width)")
 #' print(ggWide1);
 #'
 #' # The exons are required to define compressed ranges
@@ -104,23 +106,24 @@
 #' ref2c <- make_ref2compressed(test_exon_wide_gr,
 #'    nBreaks=10);
 #' ggWide1c <- ggWide1 +
-#'    scale_x_continuous(trans=ref2c$trans_grc) +
-#'    xlab("chr1 (compressed introns)") +
-#'    ggtitle("junctions (compressed introns, distorted)");
+#'    ggplot2::scale_x_continuous(trans=ref2c$trans_grc) +
+#'    ggplot2::xlab("chr1 (compressed introns)") +
+#'    ggplot2::ggtitle("junctions (compressed introns, distorted)");
 #' print(ggWide1c);
 #'
 #' # to fix the arc shapes, supply the transform to grl2df()
 #' # Note: USE THESE STEPS
-#' junc_wide_c_df <-grl2df(test_junc_wide_gr,
+#' junc_wide_c_df <- grl2df(test_junc_wide_gr,
 #'    shape="junction",
 #'    ref2c=ref2c);
-#' ggWide1c2 <- ggplot(junc_wide_c_df, aes(x=x, y=y, group=id, fill=gr_name)) +
+#' ggWide1c2 <- ggplot2::ggplot(junc_wide_c_df,
+#'    ggplot2::aes(x=x, y=y, group=id, fill=gr_name)) +
 #'    ggforce::geom_diagonal_wide(alpha=0.7) +
 #'    colorjam::theme_jam() +
 #'    colorjam::scale_fill_jam() +
-#'    scale_x_continuous(trans=ref2c$trans_grc) +
-#'    xlab("chr1 (compressed introns)") +
-#'    ggtitle("junctions (compressed introns)");
+#'    ggplot2::scale_x_continuous(trans=ref2c$trans_grc) +
+#'    ggplot2::xlab("chr1 (compressed introns)") +
+#'    ggplot2::ggtitle("junctions (compressed introns)");
 #' print(ggWide1c2);
 #'
 "test_junc_wide_gr"
@@ -136,7 +139,7 @@
 #'    exon for an arbitrary gene. It has one column of values,
 #'    `"gene_name"` used for Sashimi plot preparation.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' # The code below is used to create the exon test data
@@ -176,7 +179,7 @@
 #'    exon for an arbitrary gene. It has one column of values,
 #'    `"gene_name"` used for Sashimi plot preparation.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' # The code below is used to create the exon test data
@@ -222,7 +225,7 @@
 #' with NumericList values representing RNA-seq read coverage
 #' across these exons.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' suppressPackageStartupMessages(library(GenomicRanges));
@@ -244,7 +247,8 @@
 #' exondf <- exoncov2polygon(test_cov_gr, covNames="sample_A");
 #' gg3 <- ggplot(exondf,
 #'       aes(x=x, y=y, group=gr, fill=gr, color=gr)) +
-#'    ggforce::geom_shape(alpha=0.8) +
+#'    ggforce::geom_shape(alpha=0.8,
+#'       stat="unpack_polygon") +
 #'    colorjam::theme_jam() +
 #'    colorjam::scale_fill_jam() +
 #'    colorjam::scale_color_jam();
@@ -275,7 +279,7 @@
 #' coverage data on a genomic scale. See examples
 #' for steps to compress the intron sizes.
 #'
-#' @family splicejam data
+#' @family Splicejam data
 #'
 #' @examples
 #' # The steps below demonstrate how to create coverage data manually
@@ -291,7 +295,8 @@
 #' widecovdf <- exoncov2polygon(test_cov_wide_gr, covNames="sample_A");
 #' ggWide3 <- ggplot(widecovdf,
 #'       aes(x=x, y=y, group=gr, fill=gr, color=gr)) +
-#'    ggforce::geom_shape(alpha=0.7) +
+#'    ggforce::geom_shape(alpha=0.7,
+#'       stat="unpack_polygon") +
 #'    colorjam::theme_jam() +
 #'    colorjam::scale_fill_jam() +
 #'    colorjam::scale_color_jam();