plotSamplesMut: Plot mutations per sample distribution.

In hanasusak/cDriver: Find best driver candidate genes

Description

plot.samplesMut Function to plot samples mutation counts.

Usage

plotSamplesMut(sample.mutations, indels = TRUE, silent = TRUE,
  fill = FALSE, Tumor_Sample_Barcode = NULL, Hugo_Symbol = NULL,
  Variant_Classification = NULL, Variant_Type = NULL)

Arguments

sample.mutations	data frame in MAF like format. Columns (with exactly same names) which sample.mutations should have are: Variant_Classification column specifed by MAF format, used to distinguish between silent and nonsilent SNVs Hugo_Symbol column specifed by MAF format, which reports gene for each SNV. Tumor_Sample_Barcode column specifed by MAF format, reporting for each SNV in wich patient was found. Variant_Type columns pecifed by MAF format; is mutation SNV or InDel
indels	a boolean value indicating should indels be counted. By default it is True.
silent	a boolean value indicating should silent mutations be counted. By default it is True.
fill	a boolean value indicating should plot only represent proportion between 3 types of mutations, not counts. By default it is False.
Tumor_Sample_Barcode	(optional) integer/numeric value indicating column in sample.mutations which have sample ids for SNVs/Indels. Default is NULL value (in this case sample.mutations should already have this column)
Hugo_Symbol	(optional) integer/numeric value indicating column in sample.mutations having gene names for reported SNVs/Indels. Default is NULL value (in this case sample.mutations should already have this column)
Variant_Classification	(optional) integer/numeric value indicating column in sample.mutations which contain classification for SNV (Silent or not). Default is NULL value (in this case sample.mutations should already have this column)
Variant_Type	(optional) integer/numeric value indicating column in sample.mutations which contains indormation if mutations is SNV or InDel . Default is NULL value (in this case sample.mutations should already have this column)

Value

ggplot2 object

Examples

# plot sample's mutations , all of them
plotSamplesMut(sample.genes.mutect)
# plot proportion of silent and nonsilent, without indels
plotSamplesMut(sample.genes.mutect, indels=FALSE, fill=TRUE)

hanasusak/cDriver documentation built on May 17, 2019, 2:27 p.m.