scatterMixPlot: Generate a scatter plot with the output from mixModelParams

In oncomix: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data

Description

This function allows you to generate the parameters for two 2-component mixture models with equal variances

Usage

scatterMixPlot(mmParams, selIndThresh = 1, geneLabels = NULL)

Arguments

mmParams	The output from the mixModelParams function. Will utilize the deltaMu2 and deltaMu1 rows.
selIndThresh	This is the selectivity index threshold to use. All genes with SI values above this threshold will be highlighted in purple. Specify either selIndThresh or geneLabels (not both simultaneously).
geneLabels	A character vector of gene names used to label the genes with that name on the scatter plot. Specify either selIndThresh or geneLabels (not both simultaneously).

Value

Returns a ggplot scatter object that can be plotted

See Also

mixModelParams

Examples

exprNml <- as.data.frame(matrix(data=rgamma(n=150, shape=2, rate=2),
nrow=10, ncol=15))
colnames(exprNml) <- paste0("patientN", seq_len(ncol(exprNml)))
rownames(exprNml) <- paste0("gene", seq_len(nrow(exprNml)))

exprTum <- as.data.frame(matrix(data=rgamma(n=150, shape=4, rate=3),
nrow=10, ncol=15))
colnames(exprTum) <- paste0("patientT", seq_len(ncol(exprTum)))
rownames(exprTum) <- paste0("gene", seq_len(nrow(exprTum)))

mmParams <- mixModelParams(exprNml, exprTum)
scatterMixPlot(mmParams)

oncomix documentation built on Nov. 8, 2020, 5:39 p.m.