High Resolution Figures in R

As I was recently preparing a manuscript for PLOS ONE, I realized the default resolution of R and RStudio images are insufficient for publication. PLOS ONE requires 300 ppi images in TIFF or EPS (encapsulated postscript) format. In R plots are exported at 72 ppi by default. I love RStudio but was disappointed to find that there was no options for exporting figures at high resolution.

PLOS ONE has extensive instructions for scaling, compressing, and converting image files to meet their standards. Unfortunately, there is no good way to go from low resolution to high resolution (i.e. rescaling in Photoshop) as my friend Liam Revell, and phytools author, pointed out with entertaining illustration from PhD comics (upper right panel). The point is if the original image isn’t created at a high enough resolution, then using Photoshop to artificially increase the resolution has problems of graininess because Photoshop can only guess how to interpolate between the points. This might not be a big problem with simple plots created in R because interpolation between points in a line shouldn’t be difficult, particularly when starting with a PDF.

Even if scaling up from a low resolution PDF would work, it would be better to have a direct solution in R. It took some time to figure out but here are some trials and the ultimate solution I came up with:

x <- 1:100
y <- 1:100
plot(x, y) # Make plot
tiff("Plot1.tiff")
dev.off()

Nothing happens in this case. However, by setting up the tiff file first, then making the plot, the resulting TIFF file is saved to your working directory and is 924 KB, 72 ppi, 480 x 480 pixels.

To increase the resolution I tried the following:

tiff("Plot2.tif", res = 300)
plot(x, y) # Make plot
dev.off()

but in RStudio the plot could not be printed and hence not saved because it was too large for the print area. Therefore, I had to open up R directly and run the code. Interestingly, a blank TIFF file was created of the same size as Plot1.tiff. This is where I got hung up for a while. I eventually found that R can’t figure out the other image parameters when resolution is changes or because the default is too big to print, so they have to be specified directly as such:

tiff("Plot3.tiff", width = 4, height = 4, units = 'in', res = 300)
plot(x, y) # Make plot
dev.off()

This creates a TIFF file that is 5,800 KB, 300 ppi, 4 inches by 4 inches. Surprisingly, on a Mac it still indicates that it’s only 72 ppi when viewed in Preview. The larger size indicates that it is actually 300 ppi. I ran the same code but specifically specified res = 72 and the file was only 334 KB, suggesting that Preview is incorrect and the file is really 300 ppi. I played with various compressions but lzw and none were the same while rle resulted in a larger file (less compression). That seems odd again.

Finally, I tried using the bitmap function to create a TIFF:

bitmap("Plot7.tiff", height = 4, width = 4, units = 'in', type="tifflzw", res=300)
plot(x, y)
dev.off()
par(mfrow = c(1,1))

Interestingly, this file is only 9 KB but is listed as 300 dpi, 1200 x 1200 pixels. I’m really not sure why these functions don’t seem to be working as smoothly as expected but hopefully this can help get high resolution images directly from R for publication. I plan to use the bitmap function in the future to create high resolution TIFF files for publication. This is what is desired by outlets such as PLOS ONE. It’s easier than dealing with postscript. I also don’t know if EPS files from R or RStudio are created with LaTeX. I know that can be a problem for PLOS ONE.

 EDIT: Just found a nice blog post with recommendations on device 
outputs on Revolutions here

Below is all the code that includes comparison of sizes with PDF, PNG, JPEG, and EPS files as well.

plot(x, y) # Make plot
tiff("Plot1.tiff")
dev.off()

tiff("Plot2.tiff", res = 300)
plot(x, y) # Make plot
dev.off()

tiff("Plot3.tiff", width = 4, height = 4, units = 'in', res = 300)
plot(x, y) # Make plot
dev.off()

tiff("Plot3.72.tiff", width = 4, height = 4, units = 'in', res = 72)
plot(x, y) # Make plot
dev.off()

tiff("Plot4.tiff", width = 4, height = 4, units = 'in', res = 300, compression = 'lzw')
plot(x, y) # Make plot
dev.off()

tiff("Plot5.tiff", width = 4, height = 4, units = 'in', res = 300, compression = 'none')
plot(x, y) # Make plot
dev.off()

tiff("Plot6.tiff", width = 4, height = 4, units = 'in', res = 300, compression = 'rle')
 # Make plot
dev.off()

bitmap("Plot7.tiff", height = 4, width = 4, units = 'in', type="tifflzw", res=300)
plot(x, y)
dev.off()
par(mfrow = c(1,1))

bitmap("Plot8.tiff", height = 480, width = 480, type="tifflzw", res=300)
plot(x, y)
dev.off()
par(mfrow = c(1,1))

jpeg("Plot3.jpeg", width = 4, height = 4, units = 'in', res = 300)
plot(x, y) # Make plot
dev.off()

tiff("Plot4b.tiff", width = 4, height = 4, pointsize = 1/300, units = 'in', res = 300)
plot(x, y) # Make plot
dev.off()

png("Plot3.png", width = 4, height = 4, units = 'in', res = 300)
plot(x, y) # Make plot
dev.off()

pdf("Plot3.pdf", width = 4, height = 4)
plot(x, y) # Make plot
dev.off()

postscript("Plot3.eps", width = 480, height = 480)
plot(x, y) # Make plot
dev.off()