plotStaircase: Plot heatmap for genes-sample pairs .

Description Usage Arguments Value Examples

View source: R/plots.R

Description

plotStaircase Function to plot heatmap for genes-sample pairs orderd by genes which explain most of the patients .

Usage

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plotStaircase(sample.mutations, result.df, topGenes = 40, silent = FALSE,
  indels = TRUE, allSamples = FALSE, Tumor_Sample_Barcode = NULL,
  Hugo_Symbol = NULL, Variant_Classification = NULL, Variant_Type = NULL,
  color = "CCF", groupMax = 1, order = "frequency")

Arguments

sample.mutations

data frame in MAF like format. Columns (with exactly same names) which sample.mutations should have are:

  • Tumor_Sample_Barcode column specifed by MAF format, reporting for each SNV in wich patient was found.

  • Hugo_Symbol column specifed by MAF format, which reports gene for each SNV.

  • Variant_Classification column specifed by MAF format, used to distinguish between silent and nonsilent SNVs

  • Variant_Type columns pecifed by MAF format; is mutation SNV or InDel

result.df

a data frame with Hugo_Symbol column. Genes in this column should be ordered by importance.

topGenes

a numeric/integer value; How meny top genes from results will be ploted.

silent

a boolean value indicating should silent mutations be counted. By default it is True.

indels

a boolean value indicating should indels be counted. By default it is True.

allSamples

a boolean value indicating if all samples should be plotted.

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)

color

a numeric or character value indicating column to color the samples.

groupMax

a numeric value which will be taken as maximum value when grouping color column for samples and genes pairs.

order

a character value which can be or 'frequency' or 'CCF_sum'.

Value

ggplot2 object

Examples

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#get CCF column
sample.genes.mutect <- CCF(sample.genes.mutect)
# get background
bcgr.prob <- bcgr.combine(sample.genes.mutect)
# get ranking
df1 <- bayes.risk(sample.genes.mutect, bcgr.prob, prior.sick = 0.00007) 
df2 <- bayes.driver(sample.genes.mutect, bcgr.prob, prior.driver = 0.001) 
df.final <- combine.ranking(list(df1, df2), min.mut = 2 )
# plot boxplot of CCF for top genes
plotStaircase(sample.mutations=sample.genes.mutect, result.df=df.final)

hanasusak/cDriver documentation built on Jan. 20, 2018, 2:14 p.m.