Merge branch 'master' into RELEASE_3_18

gagneurlab · Apr 24, 2024 · 9c8a146 · 9c8a146
2 parents d00fec0 + b17d86d
commit 9c8a146
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,10 +52,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'next', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
+          - { os: windows-latest, r: '4.3', bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -106,16 +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'
@@ -249,7 +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}
@@ -313,7 +314,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-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
@@ -42,6 +42,7 @@ Imports:
     generics,
     GenomicRanges,
     ggplot2,
+    ggrepel,
     grDevices,
     heatmaply,
     pheatmap,
@@ -69,7 +70,10 @@ Suggests:
     RMariaDB,
     AnnotationDbi,
     beeswarm,
-    covr
+    covr,
+    GenomeInfoDb,
+    ggbio,
+    biovizBase
 LinkingTo:
     Rcpp,
     RcppArmadillo

diff --git a/NAMESPACE b/NAMESPACE
@@ -35,6 +35,7 @@ export(plotExpectedVsObservedCounts)
 export(plotExpressedGenes)
 export(plotExpressionRank)
 export(plotFPKM)
+export(plotManhattan)
 export(plotPowerAnalysis)
 export(plotQQ)
 export(plotSizeFactors)
@@ -53,6 +54,7 @@ exportMethods(plotAberrantPerSample)
 exportMethods(plotCountCorHeatmap)
 exportMethods(plotDispEsts)
 exportMethods(plotEncDimSearch)
+exportMethods(plotManhattan)
 exportMethods(plotQQ)
 exportMethods(plotVolcano)
 exportMethods(results)
@@ -73,6 +75,7 @@ importFrom(BiocGenerics,plotDispEsts)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bpisup)
 importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpmapply)
 importFrom(BiocParallel,bpparam)
 importFrom(BiocParallel,bpstart)
 importFrom(BiocParallel,bpstop)
@@ -95,14 +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<-")
@@ -114,10 +125,13 @@ importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,mcols)
 importFrom(SummarizedExperiment,rowData)
+importFrom(SummarizedExperiment,rowRanges)
 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)
@@ -130,6 +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)
@@ -143,6 +158,7 @@ importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(ggplot2,ylim)
+importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,abline)
 importFrom(graphics,axis)

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -27,6 +27,11 @@ setGeneric("plotAberrantPerSample", function(object, ...)
 setGeneric("plotCountCorHeatmap", function(object, ...) 
         standardGeneric("plotCountCorHeatmap"))
 
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotManhattan", function(object, ...) 
+    standardGeneric("plotManhattan"))
+
 #' @importFrom DESeq2 plotDispEsts
 #' @noRd
 #' @export

diff --git a/R/ZscoreMatrix.R b/R/ZscoreMatrix.R
@@ -1,14 +1,13 @@
 #' 
 #' Z score computation
 #' 
-#' Computes the z scores for every count in the matrix. 
-#' The z score is defined in the log2 space as follows:
-#' \ifelse{html}{
-#'     \out{z<sub>ij</sub> = (l<sub>ij</sub> - mu<sub>j</sub><sup>l</sup>)/
-#'             sigma<sub>j</sub><sup>l</sup>}}{
-#'     \deqn{z_{ij} = \frac{l_{ij} - \mu_j^l}{\sigma_j^l}}},
-#' where l is the log2 transformed normalized count and mu and sigma the 
-#' mean and standard deviation for gene j, respectively.
+#' Computes the z scores for every count in the matrix.
+#' The z score is defined in the log\eqn{_2}{[2]} space as follows:
+#' \eqn{z_{ij} = \frac{l_{ij} - \mu_j^l}{
+#'      \sigma_j^l}}{z_ij = (l[ij] - mu[j]^l)/sigma[ij]}
+#' where \code{l} is the log\eqn{_2}{[2]} transformed normalized count and 
+#' \eqn{\mu}{mu} and \eqn{\sigma}{sigma} the mean and standard deviation 
+#' for gene \code{j} and sample \code{i}, respectively.
 #' 
 #' @param ods OutriderDataSet
 #' @param ... Further arguments passed on to \code{ZscoreMatrix}.

diff --git a/R/inputCheckerFunctions.R b/R/inputCheckerFunctions.R
@@ -15,6 +15,8 @@ checkCountRequirements <- function(ods, test=FALSE){
         stop("There are genes without any read. Please filter first ",
                 "the data with: ods <- filterExpression(ods)")
     }
+    # Filter out genes that have on average less than 1 count per 100 samples.
+    # Ony affects datasets with more than 100 samples.
     filterGenes <- filterGenes | rowSums(counts(ods)) < ncol(ods)/100
     if(any(filterGenes) & isFALSE(test)){
         stop("The model requires for each gene at least 1 read ", 

diff --git a/R/method-evaluation.R b/R/method-evaluation.R
@@ -28,7 +28,7 @@ aberrant.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
 #' @param by if the results should be summarized by 'sample', 
 #'             'gene' or not at all (default).
 #' @param subsetName The name of a subset of genes of interest for which FDR 
-#'             corected pvalues have been previously computed. Those FDR values 
+#'             corected 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 ... Currently not in use.