ci(dry-run): Set up dry run to use latest version of R and bioc + fix…

… volcano plots (#124) * ci(dry-run): Set up bioc version to use latest version of R and bioc * fix(groupComparisonPlots): Fix volcano plot regarding logFC base
Vitek-Lab · May 24, 2024 · 9f1caa8 · 9f1caa8
1 parent 1d9e1ed
commit 9f1caa8
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/.github/workflows/dry-run-build.yml b/.github/workflows/dry-run-build.yml
@@ -11,7 +11,7 @@ jobs:
       - name: Setup R and Bioconductor
         uses: grimbough/bioc-actions/setup-bioc@v1
         with:
-          bioc-version: release
+          bioc-version: devel
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
       - name: Build, Install, Check

diff --git a/R/utils_groupcomparison_plots.R b/R/utils_groupcomparison_plots.R
@@ -203,7 +203,7 @@ colMin <- function(data) sapply(data, min, na.rm = TRUE)
                            limits = c(y.limdown, y.limup)) +
         labs(title = unique(label_name))
     plot = plot +
-        scale_x_continuous(paste0("Log", log_base_pval, " fold change"),
+        scale_x_continuous(paste0("Log", log_base_FC, " fold change"),
                            limits = c(-x.lim, x.lim))
     if (ProteinName) {
         if (!(length(unique(input$colgroup)) == 1 & any(unique(input$colgroup) == "black"))) {
@@ -237,12 +237,12 @@ colMin <- function(data) sapply(data, min, na.rm = TRUE)
     }
     if (is.numeric(FCcutoff)) {
         FCcutpos = data.table::setnames(data.table("sigline", 
-                                                   log(FCcutoff, log_base_pval), 
+                                                   log(FCcutoff, log_base_FC), 
                                                    seq(y.limdown, y.limup, length.out = 10), 
                                                    "dotted"),
                                         c("Protein", "logFC", log_adjp, "line"))
         FCcutneg = data.table::setnames(data.table("sigline", 
-                                                   (-log(FCcutoff, log_base_pval)), 
+                                                   (-log(FCcutoff, log_base_FC)), 
                                                    seq(y.limdown, y.limup, length.out = 10), 
                                                    "dotted"),
                                         c("Protein", "logFC", log_adjp, "line"))