Question: [How to Save plots in R] DiffBind
1
gravatar for chiefcat
23 months ago by
chiefcat110
chiefcat110 wrote:

Hi,

I'm trying to use a R package for the first time.

Does anyone know how to save/ export a plot (e.g. heatmap) in DiffBind?

Example: in there example (https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf) Heatmap was generated by

plot(tamoxifen)

or

dba.plotHeatmap(tamoxifen)

What should I add in order to save the plot directly from the command? Thanks!!

chip-seq diffbind R • 1.1k views
ADD COMMENTlink modified 23 months ago by Rory Stark510 • written 23 months ago by chiefcat110
2

This doesn't look like a bioinformatics question to me and might get closed for that reason. Meanwhile, try this:

jpeg('myimage.jpeg')
plot(tamoxifen)
dev.off()
ADD REPLYlink written 23 months ago by WouterDeCoster41k
2

Additionally, using RStudio will let you see your plots, adjust any plotting settings, and then save them as an image quite easily. Useful if you think you're going to have to mess with your figures repeatedly or if you want to view dataframes, etc directly in a table format.

Won't work on a headless server though, obviously.

ADD REPLYlink written 23 months ago by jared.andrews073.1k
3
gravatar for Rory Stark
23 months ago by
Rory Stark510
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark510 wrote:

The comment above is the correct answer to the question. Before plotting, call one of the functions that redirects the plot to a file, such as jpeg(), pdf(), or png(). After plotting, call dev.off() to close the file. You can do multiple plots before calling dev.off() and they will all end up in the same file.

ADD COMMENTlink written 23 months ago by Rory Stark510

Hi @Rory, How can we save an image from DiffBind with 300 dpi resolution.

I tried

tiff(file = "final.tiff", units = "px", res = 300)

but got an error:

Error in plot.new() : figure margins too large.

Can you please help?

Thanks!

ADD REPLYlink modified 28 days ago • written 28 days ago by Researcher40
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