plotReceptLoss: Plot histogram of genes with expression loss

In dpique/receptLoss: Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

Description

This function allows you to plot histograms of tumor and adj normal data

Usage

plotReceptLoss(exprMatrNml, exprMatrTum, rldf, geneName, addToTitle = "", clrs)

Arguments

exprMatrNml	A matrix of expression values from normal tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrTum.
exprMatrTum	A matrix of expression values from tumor tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrNml.
rldf	The dataframe output from running the receptLoss function
geneName	The name of the gene to plot. The name of the gene should correspond to a row name in both exprMatrNml and exprMatrTum matrices.
addToTitle	A string that can be added to the title, which includes the gene name.
clrs	Vector of length 2 containing colors to use for plot

Value

returns an object of class 'ggplot'

Examples

exprMatrNml <- matrix(abs(rnorm(100, mean=2)), nrow=10)
exprMatrTum <- matrix(abs(rnorm(100)), nrow=10)
geneNames <- paste0(letters[seq_len(nrow(exprMatrNml))],
seq_len(nrow(exprMatrNml)))
rownames(exprMatrNml) <- rownames(exprMatrTum) <- geneNames
nSdBelow <- 2
minPropPerGroup <- .2
rl <- receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup)
clrs <- c("#E78AC3", "#8DA0CB")
plotReceptLoss(exprMatrNml, exprMatrTum, rl, geneName="g7", clrs=clrs)

dpique/receptLoss documentation built on April 27, 2020, 3:21 a.m.