Commit 678f20d5 authored by Holger Brandl's avatar Holger Brandl

updated core_commons version.

parent 9edb5d38
...@@ -140,7 +140,7 @@ makePcaPlot = function(matrixData, color_by=NA, items=rownames(matrixData), titl ...@@ -140,7 +140,7 @@ makePcaPlot = function(matrixData, color_by=NA, items=rownames(matrixData), titl
pc12 <- data.frame(PCA1 = scores[, 1], PCA2 = scores[, 2], group = color_by_sorted) pc12 <- data.frame(PCA1 = scores[, 1], PCA2 = scores[, 2], group = color_by_sorted)
if(is.na(color_by)){ if(is.na(color_by)){
pcaPlot = ggplot(pc12, aes(PCA1, PCA2, text= paste("Sample:", items))) + geom_point(alpha = .4) pcaPlot = ggplot(pc12, aes(PCA1, PCA2, text= paste("Sample:", items))) + geom_point(alpha = .75)
}else{ }else{
pcaPlot = ggplot(pc12, aes(PCA1, PCA2, color = group, text=paste("Sample:", items))) + geom_point(alpha = .4) pcaPlot = ggplot(pc12, aes(PCA1, PCA2, color = group, text=paste("Sample:", items))) + geom_point(alpha = .4)
} }
...@@ -225,7 +225,7 @@ gp_bin2d <- function(data, mapping, ..., low = "#10721C", high = "#F11D05") { ...@@ -225,7 +225,7 @@ gp_bin2d <- function(data, mapping, ..., low = "#10721C", high = "#F11D05") {
######################################################################################################################## ########################################################################################################################
### Base-plot utils ### Base-plot utils
# https://stackoverflow.com/questions/15282580/how-to-generate-a-number-of-most-distinctive-colors-in-r
plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"), ...); expr; dev.off(); } plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"), ...); expr; dev.off(); }
#plotPDF("test", plot(1:10)) #plotPDF("test", plot(1:10))
...@@ -242,4 +242,3 @@ create_palette <- function(x, pal = 'Set1'){ ...@@ -242,4 +242,3 @@ create_palette <- function(x, pal = 'Set1'){
setNames(brewer.pal(name = pal, n = n)[1:n], ux) setNames(brewer.pal(name = pal, n = n)[1:n], ux)
} }
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment