Unknown graphics device error in Rstudio

Question

I want to save 10 different ggplots to disc with different parameters, but getting the error:

Error: Unknown graphics device ''

Here is my code:

for (geneNum in 1:10) {
  geneCounts <- plotCounts(dds, gene=gene_list[geneNum], 
  intgroup=c("Groups","Mouse"), returnData=TRUE)
  ggplot(geneCounts, aes(x=Mouse, y=count, color=Groups, 
  group=Groups)) +
  scale_y_log10() + geom_point(size=3) + geom_line() + 
  ggtitle(gene_list[geneNum])
  filename <- paste0("gene", geneNum, sep="_")
  ggsave(filename,
     plot = last_plot(), # or give ggplot object name as in myPlot,
     width = 5, height = 5,
     units = "in", # other options c("in", "cm", "mm"), 
     dpi = 300)
}

Any suggestions would be greatly appreciated.

Answer 1

(Copied from Alistaire's comment.)

ggsave() looks for the file extension on the filename, e.g. .png, and uses the appropriate (what R calls) graphics device to save the image (really, the kind of system used to encode the image data, PNG, BMP, JPG, PDF etc.). This error is usually caused by a missing or incorrect file extension in the filename. Specifically, in your case,

change

filename <- paste0("gene", geneNum, sep="_")

to e.g. (for .png output):

filename <- paste0("gene", geneNum, ".png", sep="_")