Update gha and update documentation (#63)

* adapt github actions to use new BIOC versions and use always variables * document arg and fix import warnings --------- Co-authored-by: Christian Mertes <[email protected]>
gagneurlab · Apr 24, 2024 · b17d86d · b17d86d
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -107,16 +107,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -250,7 +250,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
               build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
+              error_on = "warning",
               check_dir = "check"
           )
         shell: Rscript {0}
@@ -314,7 +314,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
+          name: ${{ runner.os }}-biocversion-${{ runner.bioc }}-r-${{ runner.r }}-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -72,7 +72,8 @@ Suggests:
     beeswarm,
     covr,
     GenomeInfoDb,
-    ggbio
+    ggbio,
+    biovizBase
 LinkingTo:
     Rcpp,
     RcppArmadillo

diff --git a/NAMESPACE b/NAMESPACE
@@ -98,15 +98,22 @@ importFrom(DESeq2,sizeFactors)
 importFrom(GenomicFeatures,exonsBy)
 importFrom(GenomicFeatures,makeTxDbFromGFF)
 importFrom(GenomicRanges,GRanges)
+importFrom(GenomicRanges,end)
+importFrom(GenomicRanges,findOverlaps)
 importFrom(GenomicRanges,reduce)
+importFrom(GenomicRanges,start)
 importFrom(GenomicRanges,width)
 importFrom(IRanges,IRanges)
 importFrom(PRROC,pr.curve)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(S4Vectors,"metadata<-")
+importFrom(S4Vectors,"values<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,endoapply)
 importFrom(S4Vectors,metadata)
+importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,subjectHits)
+importFrom(S4Vectors,values)
 importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,"assays<-")
 importFrom(SummarizedExperiment,"colData<-")
@@ -123,6 +130,8 @@ importFrom(generics,fit)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_abline)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_histogram)
@@ -135,6 +144,7 @@ importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,quo_name)
 importFrom(ggplot2,scale_color_brewer)
 importFrom(ggplot2,scale_color_identity)
 importFrom(ggplot2,scale_color_manual)

diff --git a/R/method-plot.R b/R/method-plot.R
@@ -55,6 +55,8 @@
 #'             corrected pvalues were previously computed. Those FDR values 
 #'             on the subset will then be used to determine aberrant status. 
 #'             Default is NULL (using transcriptome-wide FDR corrected pvalues).
+#' @param chr The chromosomes to be displayed in the \code{plotManhattan} 
+#'             function. Default is \code{NULL}, i.e. all chromosomes are shown. 
 #### Graphical parameters
 #' @param main Title for the plot, if missing a default title will be used.
 #' @param groups A character vector containing either group assignments of
@@ -1341,8 +1343,8 @@ plotManhattan.OUTRIDER <- function(object, sampleID, value="pvalue",
                                    featureRanges=rowRanges(object), 
                                    subsetName=NULL,
                                    chrColor = c("black", "darkgrey")){
-    require(ggbio)
-    require(GenomeInfoDb)
+    requireNamespace("ggbio")
+    requireNamespace("GenomeInfoDb")
 
     # check user input
     checkOutriderDataSet(object)
@@ -1406,13 +1408,13 @@ plotManhattan.OUTRIDER <- function(object, sampleID, value="pvalue",
         if(any(grepl("chr", chr))){
             chr <- gsub("chr", "", chr)
         }
-        if(!all(chr %in% unique(seqnames(gr)))){
+        if(!all(chr %in% unique(GenomeInfoDb::seqnames(gr)))){
             stop("Not all chromosomes selected for subsetting are present ",
                  "in the GRanges object.")
         }
 
         # subset
-        gr <- gr[as.character(seqnames(gr)) %in% chr]
+        gr <- gr[as.character(GenomeInfoDb::seqnames(gr)) %in% chr]
 
         # add chr to plot title if only one chr given
         if(length(chr) == 1){
@@ -1458,6 +1460,7 @@ plotGrandLinear.adapted <- function (obj, ..., facets, space.skip = 0.01,
         highlight.overlap = c("any", "start", "end", "within", "equal"),
         spaceline = FALSE,
         use.genome.coords=TRUE){
+    requireNamespace("biovizBase")
     if (is.null(geom)) 
         geom <- "point"
     args <- list(...)
@@ -1502,7 +1505,7 @@ plotGrandLinear.adapted <- function (obj, ..., facets, space.skip = 0.01,
     if (!is.null(cutoff)) 
         p <- p + geom_hline(yintercept = cutoff, color = cutoff.color, 
                             size = cutoff.size)
-    chrs <- names(seqlengths(obj))
+    chrs <- names(GenomeInfoDb::seqlengths(obj))
     if (.is.seq) {
         N <- length(chrs)
         cols <- rep(.color, round(N/length(.color)) + 1)[1:N]
@@ -1521,7 +1524,7 @@ plotGrandLinear.adapted <- function (obj, ..., facets, space.skip = 0.01,
         highlight.overlap <- match.arg(highlight.overlap)
         idx <- findOverlaps(obj, highlight.gr, type=highlight.overlap)
         .h.pos <- lapply(split(queryHits(idx), subjectHits(idx)), function(id) {
-            gr <- GRanges(as.character(seqnames(p@data))[id][1], 
+            gr <- GRanges(as.character(GenomeInfoDb::seqnames(p@data))[id][1], 
                 IRanges(start = min(start(p@data[id])), 
                         end = max(end(p@data[id]))))
                 val <- max(as.numeric(values(p@data[id])[, quo_name(args.aes$y)]))
@@ -1541,8 +1544,10 @@ plotGrandLinear.adapted <- function (obj, ..., facets, space.skip = 0.01,
                     do.call(aes, list(x = substitute(midpoint), y = args.aes$y)), 
                     color = highlight.col)
             if (!is.null(highlight.name)) {
-                seqlevels(.h.pos, pruning.mode = "coarse") <- seqlevels(obj)
-                suppressWarnings(seqinfo(.h.pos) <- seqinfo(obj))
+                GenomeInfoDb::seqlevels(.h.pos, pruning.mode = "coarse") <- 
+                    GenomeInfoDb::seqlevels(obj)
+                suppressWarnings(GenomeInfoDb::seqinfo(.h.pos) <- 
+                                    GenomeInfoDb::seqinfo(obj))
                 .trans <- biovizBase::transformToGenome(.h.pos, space.skip = space.skip)
                 values(.trans)$mean <- (start(.trans) + end(.trans))/2
                 values(.trans)$names <- highlight.name

diff --git a/R/package-OUTRIDER.R b/R/package-OUTRIDER.R
@@ -28,14 +28,15 @@
 #' 
 #' @importFrom GenomicFeatures makeTxDbFromGFF exonsBy
 #' 
-#' @importFrom GenomicRanges GRanges reduce width 
+#' @importFrom GenomicRanges GRanges reduce width start end findOverlaps 
 #' 
 #' @importFrom ggplot2 ggplot aes annotate geom_bar geom_histogram 
 #'          geom_hline geom_smooth geom_point labs scale_x_log10 
 #'          scale_y_log10 scale_fill_manual scale_color_manual 
 #'          scale_fill_brewer scale_color_brewer theme ylim 
 #'          ggtitle geom_vline geom_text scale_linetype_manual geom_line 
-#'          geom_abline theme_bw element_blank xlab ylab scale_color_identity
+#'          geom_abline theme_bw element_blank xlab ylab scale_color_identity 
+#'          facet_grid facet_wrap quo_name
 #' 
 #' @importFrom ggrepel geom_text_repel
 #' 
@@ -62,7 +63,8 @@
 #' 
 #' @importFrom reshape2 melt
 #' 
-#' @importFrom S4Vectors DataFrame metadata metadata<- endoapply
+#' @importFrom S4Vectors DataFrame metadata metadata<- endoapply queryHits
+#'          subjectHits values values<-
 #' 
 #' @importFrom scales math_format trans_format
 #' 
@@ -128,5 +130,10 @@ globalVariables(package="OUTRIDER", c(
         "Var2",
         ".x",
         "y",
-        "z"))
+        "z",
+        "AberrantByGene",
+        "AberrantBySample",
+        "FDR_set",
+        "aberrantLabel",
+        "geneID"))
 
diff --git a/man/plotFunctions.Rd b/man/plotFunctions.Rd