waterfallPlot: waterfallPlot: Create visualisations from BEEM output

In BiSEp: Toolkit to Identify Candidate Synthetic Lethality

Description

Takes the output from the function BISEP and a discreet mutation matrix as input. The mutation matrix samples (columns) must mirror or overlap with the gene expression matrix. The data in the mutation matrix must be a discreet 'WT' or 'MUT' call based on the status of each gene with each sample. Gene names must be available in the input matrices.

Usage

waterfallPlot(
	bisepData=data, 
	mutData=mutData, 
	expressionGene, 
	mutationGene
	)

Arguments

bisepData	This should be the output from the BISEP function.
mutData	This should be a matrix with genes rownames and samples as column names. All cells should be made up of a discreet 'WT' or 'MUT' call. There should be overlap (by sample) with the gene expression matrix.
expressionGene	The gene whose expression you would like to plot.
mutationGene	The gene whose mutation status you would like to overlap with the expression gene.

Details

The function will return an error if any of the input information is incorrect or missing. The resulting plot will be returned in real time.

Value

A waterfall plot. The plot is made up of two panels: the left panel is a density distribution of the expression gene provided and the right panel is a bar-chart of the gene expression level coloured by mutation status.

Author(s)

Mark Wappett

Examples

data(BISEP_data)
data(MUT_data)
waterfallOut <- waterfallPlot(BISEP_data, MUT_data, expressionGene="micb", mutationGene="PBRM1")

BiSEp documentation built on May 2, 2019, 9:13 a.m.