CODEWITHSUNDEEP
rpdfggplot2
Kaston
Kaston

Reputation: 51

R error saving ggplot pdf

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?

Upvotes: 5

Views: 17728

Answers (7)

Andreas Flensmark
Andreas Flensmark

Reputation: 1

I had the same problem, I fixed it by moving the working directory, since it thought it was in system32.

If you are working in Rstudio

  • Session
  • Set working directory
  • Desktop

and either make a new folder or choose an existing one

Upvotes: 0

Olympia
Olympia

Reputation: 537

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.

Upvotes: 1

DMick2013
DMick2013

Reputation: 21

I just got this error while running a for loop to create many pdf files containing charts.

For me, the error was resolved when I simply closed out of the one pdf file I opened earlier to examine my output. R was throwing the error because I had the file open, so it could not overwrite it. It is another plausible cause for this error.

Upvotes: 1

Srijan Chaudhary
Srijan Chaudhary

Reputation: 697

T faced the same issue and found out that the here() is not pointing to the correct directory in which the R script file is. Solution to this is, either try to point the here() to the correct directory or close\quit the R studio and open the script directly in R studio i.e. Open the R studio fresh then, here() will automatically point to the same directory as to that of the script.

Upvotes: 0

user1302884
user1302884

Reputation: 843

One of the reasons for Error in grDevices::pdf is write permissions. Proper write permissions should solve the issue. - chmod 777 -R dirname

Upvotes: 0

user8376075
user8376075

Reputation: 31

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.

Upvotes: 3

Johan Larsson
Johan Larsson

Reputation: 3694

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.

Upvotes: 3

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