R error saving ggplot pdf

Question

When I try to save a plot made using ggplot as a pdf using this code:

library(ggplot2)

file = "/data/mda/20150630-1Mb-full_comparison-low_depth_hTERT/result/comparison_figure/SD_rank_custom.csv"
figure_file = "/data/mda/20150604-1Mb-full_comparison-low_depth_hTERT/result/comparison_figure/SD_rank_custom.pdf"

sd_data <- as.data.frame(read.csv(file, header=TRUE))

# generate box plot
ggplot(
    data=sd_data,
    aes(
        x=Experiment, 
        y=SD
    )
)+  
theme_bw() + #use bw theme
geom_boxplot(outlier.shape = NA) + #hide outlier points
geom_jitter() + 
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))   

ggsave(
  filename=figure_file,
  width=10,
  height=10
)

I get the following error:

Error in grDevices::pdf(..., version = version) :

cannot open file 'file.pdf'

Calls: ggsave -> device ->

Execution halted

I think my version of R was recently updated to 3.2.0, and I've confirmed that it works fine in v3.1.1 so I'm assuming this is version related. I also confirmed I can write a csv file to the directory.

Any ideas how to fix this?

Solution 1

I think you're trying to write to a non-existent folder, and as far as I know grDevices won't allow this. Someone else seems to have a similar issue.

I tried your code both in R 3.1.1 and 3.2.1—they both give the same error (unless the directory is created on beforehand.

You could try adding the following line of code:

dir.create(file.path(dirname(figure_file)))

It will create the directory for you.

Solution 2

I had the same, turned out I had already an object with the same name saved in that directory that apparently does not get overwritten.

Solution 3

I got the same error when my file name was too long - and therefore the path name in windows exceeded the allowed letters limit. Shortening the file name solved this issue.