BiSEp (version 2.3)

waterfallPlot: waterfallPlot: Create visualisations from BEEM output

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
	)

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.

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.

Author

Mark Wappett

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.

Examples

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