Create tSNE, UMAP plots as pdfs

Question

Create tSNE, UMAP plots as pdfs

Closed this issue 4 years ago · 4 comments

An attempt has been made at having the pipeline produce pdf files of the following plots:

pca
tSNE
UMAP
DE Heatmap

However, having the pipeline create and output the plots in parallel is presenting challenges. As of now, the code tries to store the plots in a list, and outside of the foreach loop print them to disk like so:

for ( pdffile in pdfs ) {
 
  pdf(pdffile)
  pdfs[[pdffile]]
  dev.off()

}

This produces no image files.
Investigate R best-practices for this and implement them.

Answer 1 · 2020-06-08T13:53:49.000Z

Consider using .combine with the foreach %dopar% to get the plots out of the loop.

Answer 2 · 2020-06-22T13:55:36.000Z

make the dimensions 10x10, pt size 2 should be default for the sizes.

Answer 3 · 2020-08-03T13:45:53.000Z

try ggsave

Answer 4 · 2020-08-07T22:03:37.000Z

ggsave is writing pdf's as expected from within the %dopar% loop.

(Edited to remove comment that duplicates another issue)