plotSamplesMut: Plot mutations per sample distribution.

Description Usage Arguments Value Examples

View source: R/plots.R

Description

plot.samplesMut Function to plot samples mutation counts.

Usage

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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

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# 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 Jan. 20, 2018, 2:14 p.m.