Update gsea plot functions to allow more arguments for gseaplot2.

DavisLaboratory · Jan 12, 2024 · c9f9cee · c9f9cee
1 parent 8ea0762
commit c9f9cee
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Showing 5 changed files with 20 additions and 12 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,8 +53,8 @@ jobs:
       matrix:
         config:
           # - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: '4.3.2', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          # - { os: ubuntu-latest, r: 'devel', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          # - { os: ubuntu-latest, r: '4.3.2', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
           # - { os: ubuntu-latest, r: '4.3.2', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
           # - { os: macOS-latest, r: '4.3.2', bioc: '3.18'}
           # - { os: windows-latest, r: '4.3.2', bioc: '3.18'}

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -484,7 +484,7 @@ setGeneric(
 #' @param digits num, specify the number of significant digits of pvalue table
 #' @param rank_stat character, specify which metric used to rank for GSEA,
 #'                  default "logFC"
-#' @param ... params for function [get_de_table()]
+#' @param ... params for function [get_de_table()] and function [enrichplot::gseaplot2()]
 #'
 #' @return patchwork object for all comparisons
 #'

diff --git a/R/plot.R b/R/plot.R
@@ -615,18 +615,26 @@ gsea_analysis <- function(tDEG, gsets, gene_id = "SYMBOL",
   return(gse)
 }
 ## gseaplot
-gsea_plot_init <- function(gse, pvalue_table = FALSE) {
+gsea_plot_init <- function(gse, pvalue_table = FALSE, ...) {
+  ## check params
+  pars_def <- formals(enrichplot::gseaplot2)
+  pars <- modifyList(
+    pars_def, ## default params for gseaplot2 function
+    list(...) ## new params list
+  )
+  pars <- pars[names(pars) %in% names(pars_def)]
+
   p <- lapply(names(gse), function(n) {
     if (is.null(gse[[n]])) {
       ms <- paste("No term was found enriched in", n, ".")
       message(ms)
       p <- ggpubr::as_ggplot(grid::textGrob(ms))
     } else {
-      p <- enrichplot::gseaplot2(gse[[n]],
-        geneSetID = seq_len(nrow(gse[[n]])),
-        pvalue_table = pvalue_table,
-        title = n
-      )
+      pars_new <- modifyList(pars, list(x = gse[[n]],
+                                        geneSetID = seq_len(nrow(gse[[n]])),
+                                        pvalue_table = pvalue_table,
+                                        title = n))
+      p <- do.call(enrichplot::gseaplot2, pars_new)
       p <- patchwork::wrap_elements(patchwork::wrap_plots(p, ncol = 1))
       # ## add pvalue_table
       # p <- p - patchwork::inset_element(gridExtra::tableGrob(

diff --git a/R/sig_gseaplot-methods.R b/R/sig_gseaplot-methods.R
@@ -45,7 +45,7 @@ setMethod(
     )
 
     if (method == "gseaplot") {
-      p <- gsea_plot_init(gse, pvalue_table = pvalue_table)
+      p <- gsea_plot_init(gse, pvalue_table = pvalue_table, ...)
     } else {
       p <- gsea_dotplot_init(gse, col = col, size = size)
     }
@@ -103,7 +103,7 @@ setMethod(
     )
 
     if (method == "gseaplot") {
-      p <- gsea_plot_init(gse, pvalue_table = pvalue_table)
+      p <- gsea_plot_init(gse, pvalue_table = pvalue_table, ...)
     } else {
       p <- gsea_dotplot_init(gse, col = col, size = size)
     }

diff --git a/man/sig_gseaplot.Rd b/man/sig_gseaplot.Rd