Merge pull request #7 from computproteomics/devel

Devel

Author: veitveit

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PolySTest
 Title: PolySTest: Detection of differentially regulated features. Combined 
       statistical testing for data with few replicates and missing values
-Version: 1.7.1
+Version: 1.7.2
 Authors@R: 
     person("Veit", "Schwämmle", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9708-6722"))

R/Visualizations.R

@@ -517,6 +517,12 @@ plotUpset <- function(fulldata, qlim = 0.05, fclim = c(0, 0)) {
         names(tcols) <- rep(paste("A", seq_len(NumComps)), 1)
 
         if (length(WhereRegs) > 0) {
+            # Reduce to first comparison when too many comparisons
+            if (ncol(WhereRegs) > 18) {
+                WhereRegs <- WhereRegs[, seq_len(18), drop = FALSE]
+                tcolnames <- tcolnames[seq_len(18)]
+                tcols <- tcols[seq_len(18)]
+            }
             message("Plotting upset plots")
             upset_plot <- UpSetR::upset(as.data.frame(WhereRegs),
                 nsets = ncol(WhereRegs),

inst/shiny/server.R

@@ -747,7 +747,7 @@ shinyServer(function(input, output, clientData, session) {
           paste("VolcanoPlots", Sys.Date(), ".pdf", sep="");
         },
         content = function(file) {
-          pdf(file,height=12,width=20)
+          pdf(file,height=4*Comps$num,width=20)
           plotVolcano(fulldata, compNames, testNames2, sel_prots, qlim, fclim)
           dev.off()
         }
@@ -917,7 +917,7 @@ shinyServer(function(input, output, clientData, session) {
           paste("PvalueDistrPlots", Sys.Date(), ".pdf", sep="");
         },
         content = function(file) {
-          pdf(file,height=12,width=20)
+          pdf(file,height=4*Comps$num,width=20)
           plotPvalueDistr(fulldata, compNames, testNames)
           dev.off()
         }