Question: Observing composition of somatic signatures as barcharts
gravatar for arsala521
3.2 years ago by
arsala52110 wrote:


I am using SomaticSignature package in my study. After decomposition and inferring of signatures, I tried to visualize the signatures as heatmap and as barchart. The hetamap was generated successfully but not the barchart.

I used the following command to construct barchart:

plotSignatures(sigs_pca) + ggtitle("Somatic Signatures: PCA - Barchart")

The pdf file of R plot was generated but the size of the file was zero.

Can someone kindly tell me how to solve this problem?


somaticsignatures • 420 views
ADD COMMENTlink written 3.2 years ago by arsala52110

Can you please provide a reproducible example of this, especially covering how you save the plot as a pdf file?

ADD REPLYlink written 3.2 years ago by Julian Gehring1.3k

Actually for the previous plots I constructed, things worked simply in the way that when I entered the command for plotting, the accurate pdf file of the plot was created in the working directory. However things didn't go well so smoothly with this command and file created in working directory had zero size. But when I used another method for saving the R plot, I got the correct files of the plot.

ADD REPLYlink written 3.2 years ago by arsala52110

I'm not sure if I can follow, would you be interested in giving us an example for what worked and what not? If the plots produced by the package, I would be interested in improving this. If it is related to the method how you saved the plot, it will also be helpful to other users to see what the problem is. 

ADD REPLYlink written 3.2 years ago by Julian Gehring1.3k
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