diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index ff9f936..864d79b 100644 --- a/.github/workflows/check-bioc.yml +++ b/.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: diff --git a/R/method-plot.R b/R/method-plot.R index b82c28a..39368b2 100644 --- a/R/method-plot.R +++ b/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 diff --git a/man/plotFunctions.Rd b/man/plotFunctions.Rd index d1c144b..f5caf65 100644 --- a/man/plotFunctions.Rd +++ b/man/plotFunctions.Rd @@ -174,7 +174,8 @@ plotSizeFactors(ods, basePlot = TRUE) subsetName = NULL, chrColor = c("black", "darkgrey"), padjCutoff = 0.05, - zScoreCutoff = 0 + zScoreCutoff = 0, + highlight.label.size = 5 ) } \arguments{ @@ -288,7 +289,11 @@ features that are shown in the manhattan plot.} \item{chrColor}{A vector of length 2 giving the two colors used for coloring alternating chromosomes in the manhattan plot. Default colors are 'black' and 'darkgrey'.} + +\item{highlight.label.size}{Size of the label of the highlighted genes. +Default value is 5.} } + \value{ If base R graphics are used nothing is returned else the plotly or the gplot object is returned.