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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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oncoplot for Variant_Classification of UNKNOWN #37

Closed crazyhottommy closed 7 years ago

crazyhottommy commented 7 years ago

Hi,

For my maf file, some variants are classified as UNKNOWN by annovar. on the oncoplot, it does not have any color showing it.

Thanks, Ming

PoisonAlien commented 7 years ago

Hi Ming,

By default oncoplot colors variant classifications according to MAF specififcations. UNKNOWN is not one of the standard variant classifications. You will have to manually specify color codes for them. Here are the default ones.

c('Nonstop_Mutation','Frame_Shift_Del','IGR','Missense_Mutation','Silent','Nonsense_Mutation',                   'RNA','Splice_Site','Intron','Frame_Shift_Ins','Nonstop_Mutation','In_Frame_Del','ITD','In_Frame_Ins',  'Translation_Start_Site',"Multi_Hit", 'Amp', 'Del')
crazyhottommy commented 7 years ago

Thanks! I guess I need to customize the plot by complexHeatmap. how to get the matrix for plotting oncoplot? If I specify writeMatrix =T, where can I get the matrix?

PoisonAlien commented 7 years ago

It should be in your working directory under the name onco_matrix.txt

crazyhottommy commented 7 years ago

Thanks, I found it. may be good to clarify in the documentation.