rainfallPlots is missing. about sigprofilerclusters

[ebergstr]

Hi,

You will need to set subClassify=True. The rainfall plot relies on the subclassifications of clustered events, so without these categories, the rainfall plot is not produced.

I will close this issue, but please feel free to reopen if you experience further issues!

[xysj1989]

Thanks for your reply. This time I try the following commands:

hp.analysis("BRCA", "GRCh37", "96", ["96"], subClassify=True, Output_Dir)

hp.analysis("BRCA", "GRCh37", "96", ["288"], Output_Dir, analysis="all", sortSims=True, subClassify=True, correction=True, calculateIMD=True, max_cpu=4, TCGA=True, sanger=False)

But the rainfall plot is still missing.

Here is the output from my terminal, with no errors reported.

======================================
Beginning SigProfilerClusters Analysis

Calculating mutational distances...Completed!
Determining sample-dependent intermutational distance (IMD) cutoff...Completed!

Analyzing clustered mutations...
Starting matrix generation for SNVs and DINUCs...Completed! Elapsed time: 2.06 seconds.
Matrices generated for 1 samples with 0 errors. Total of 2257 SNVs, 701 DINUCs, and 0 INDELs were successfully analyzed.

Analyzing non-clustered mutations...
Starting matrix generation for SNVs and DINUCs...Completed! Elapsed time: 1.83 seconds.
Matrices generated for 1 samples with 0 errors. Total of 1198 SNVs, 0 DINUCs, and 0 INDELs were successfully analyzed.

Plotting SigProfilerClusters Results...Completed!

[MousumyCSE]

Hi,
Can you please add a forward slash(/) when you mentioned the output directory and run again?
For example: Output_Dir = "/Users/z-1-Test/SigProfilerClusters-test/"

Hope that solve your problem and let me know if you had any issues.

[xysj1989]

Hi, Can you please add a forward slash(/) when you mentioned the output directory and run again? For example: Output_Dir = "/Users/z-1-Test/SigProfilerClusters-test/"

Hope that solve your problem and let me know if you had any issues.

The code works now! Thanks very much for your reply!
This is really an interesting point. Without the slash, everything goes well, except for subclassification.