Merge pull request #74 from gagneurlab/AtaJadidAhari-patch-bioc

Bioc new version

.github/workflows/check-bioc.yml

@@ -53,10 +53,10 @@ jobs:
       matrix:
         config:
           # 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: '4.4', bioc: '3.19'}
-          - { os: windows-latest, r: '4.4', bioc: '3.19'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:

R/method-plot.R

@@ -57,6 +57,8 @@
 #'             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. 
+#' @param highlight.label.size Size of the label of the highlighted genes to be 
+#'             displayed in the \code{plotManhattan}. Default value is 5.
 #### 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