Remove Pearson's correlation from SPLOM of q-values

Valkenborg · Feb 15, 2023 · f9bbfdc · f9bbfdc
1 parent 8ea951b
commit f9bbfdc
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/util/pairs_panels_idline.R b/util/pairs_panels_idline.R
@@ -1,5 +1,6 @@
 # just copy & paste from pairs.panels source code
 # y=x identity line instead of lm=T
+# when cor = FALSE, then upper.panel = NULL
 # col.points and cex.points arg added when lm=TRUE
 
 pairs.panels.idline <- function (x, smooth = TRUE, scale = FALSE, density = TRUE, ellipses = TRUE, 
@@ -240,13 +241,13 @@ pairs.panels.idline <- function (x, smooth = TRUE, scale = FALSE, density = TRUE
             lower.panel = panel.smoother, pch = pch, ...)
     }
     else {
-      pairs(x, diag.panel = panel.hist.density, upper.panel = panel.smoother, 
+      pairs(x, diag.panel = panel.hist.density, upper.panel = NULL, 
             lower.panel = panel.smoother, pch = pch, ...)
     }
   }
   else {
     if (!cor) {
-      pairs(x, diag.panel = panel.hist.density, upper.panel = panel.lm, 
+      pairs(x, diag.panel = panel.hist.density, upper.panel = NULL, 
             lower.panel = panel.lm, pch = pch, ...)
     }
     else {

diff --git a/util/plotting_functions.R b/util/plotting_functions.R
@@ -226,7 +226,9 @@ source('util/pairs_panels_idline.R')
 
 scatterplot_ils <- function(dat, cols, stat, spiked.proteins, refCond){
   select.stat <- match.arg(stat, c('p-values', 'log2FC', 'q-values'))
-  title <- paste("Pearson's correlation of", select.stat)
+  if (select.stat == 'log2FC') {
+    title <- paste("Pearson's correlation of", select.stat)
+  } else title = ''
   contrast.names <- unlist(lapply(stri_split(cols, fixed='_'), function(x) x[2]))
 
   # align rows (proteins) between DEA variants