A weird oncoplot in Tronco

[MaryGoAround]

Hi

I have written my maf file to a txt attached here

maf.txt

> maf=read.table("maf.txt",sep = "\t")
> maf1=maf[1:100,]
>maf2=maf[101:296,]
>maf1$Tumor_Sample_Barcode=gsub("test","try",maf1$Tumor_Sample_Barcode)
> maf=rbind(maf1,maf2)
>dataset_maf = import.MAF(maf,merge.mutation.types = FALSE)
 *** Importing from dataframe
 Loading MAF dataframe ...DONE
 *** Mutations names: using Hugo_Symbol
 *** Using full MAF: #entries  296 
         *** MAF report: TCGA=TRUE
 Type of annotated mutations: 
         [1] "Frame_Shift_Del"   "Frame_Shift_Ins"   "Nonsense_Mutation" "In_Frame_Del"      "In_Frame_Ins"     
 [6] "Unknown"          
 *** [merge.mutation.types = T] Mutations will be merged and annotated as 'Mutation'
 Number of samples: 2 
 [TCGA = TRUE] Number of TCGA patients: 2 
 Number of annotated mutations: 296 
 Mutations annotated with "Valid" flag (%): missing flag
 Number of genes (Hugo_Symbol): 181 
 Starting conversion from MAF to 0/1 mutation profiles (1 = mutation) :2 x 181 
 ........................................................................................................................................................................................................................................................................................................
 Starting conversion from MAF to TRONCO data type.
 Warning message:
         In valid.calls(maf) : Missing Validation_Status flag in MAF file.
 > oncoprint(dataset_maf)
 *** Oncoprint for ""
 with attributes: stage = FALSE, hits = TRUE
 Sorting samples ordering to enhance exclusivity patterns.
 Setting automatic row font (exponential scaling): 2
 >

I get this plot

Please help me to know where I am doing wrong

Thanks for any help

[danro9685]

Dear @MaryGoAround,

It seems that you only have 2 samples selected, that do not share mutations among them. To this end, the oncoprint seems fine. Let me know if there is anything I am missing.

Best, Daniele