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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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Oncostrip: sort columns by mutations #111

Closed maoge2333 closed 6 years ago

maoge2333 commented 6 years ago

Hi,

I am trying to sort columns by types of mutations(i.e., color), instead randomly distributed. I can't find that functionality. Could you please let me know if you have the functionality? If not, perhaps you could give me guidance to create one?

maoge2333 commented 6 years ago

and also in oncoplot, I tried to use sortbymutaion = T, but the result doesn't have any difference with sortbymutation = F. I would appreciate it if you can help me. Thanks and best regards.

PoisonAlien commented 6 years ago

Hello, Could you post your command and sessionInfo ? If you want to sort by columns you will have to make an annotation table for every sample and then sort it by sortByAnnottaion = TRUE. See here

maoge2333 commented 6 years ago

Hi, Thank for your response.

this is my command: require(maftools) ucs <- read.maf('/Users/maoge/Desktop/PR_TCGA_UCS_PAIR_Capture_All_Pairs.aggregated.capture.tcga.uuid.curated.somatic.maf') oncoplot(ucs,sortByMutation = T)

and sessionInfo: sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.2

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] maftools_1.4.15 Biobase_2.38.0 BiocGenerics_0.24.0

could you please let me know what information should be concluded in the annotation table. Thanks!

PoisonAlien commented 6 years ago

Hi, annotation table should be two columns data frame or a text file with sample names and associated annotations. Something like this.

>getClinicalData(x = laml)[,1:2]
     Tumor_Sample_Barcode FAB_classification
  1:         TCGA-AB-2802                 M4
  2:         TCGA-AB-2803                 M3
  3:         TCGA-AB-2804                 M3
  4:         TCGA-AB-2805                 M0
  5:         TCGA-AB-2806                 M1
 ---                                        
188:         TCGA-AB-3007                 M3
189:         TCGA-AB-3008                 M1
190:         TCGA-AB-3009                 M4
191:         TCGA-AB-3011                 M1
192:         TCGA-AB-3012                 M3