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.
(Copied from Alistaire's comment.)
ggsave()
looks for the file extension on the filename, eg .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 eg (for .png
output):
filename <- paste0("gene", geneNum, ".png", sep="_")
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