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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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Getting error in lollipop plot #1016

Closed MaryGoAround closed 7 months ago

MaryGoAround commented 7 months ago

Hi

As I am working with genomic England data, I am not able to copy paste my commond and the error

Please, look at this screenshot which shows the error I get and if possible help me to know the reason.

FYI, the data is whole genome sequencing data comes from germline mutations in regulatory regions of a gene.

Screenshot 2024-04-22 at 16 31 40

Thanks for any help

PoisonAlien commented 7 months ago

Hi,

The error message is pretty clear. The position you are trying to label does not exist in the maf file.

MaryGoAround commented 7 months ago

Hi,

The error message is pretty clear. The position you are trying to label does not exist in the maf file.

But you are seeing the amino acid in the screen shot in HGVps_Shortcolumn

PoisonAlien commented 7 months ago

Hi, The error is not about the column HGVSp_Short but the position you are trying to label. There are no mutations at the position 882. Remove the argument labelPos = 882 or change it to 31 as suggested.