e50-plotPurity: Plot tumor purity

In estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

Description

Plot tumor purity based on ESTIMATE score.

Usage

plotPurity(scores,
           samples="all_samples",
           platform = c("affymetrix", "agilent", "illumina"),
           output.dir="estimated_purity_plots")

Arguments

scores	a GCT file output by estimateScore method containing stromal, immune, ESTIMATE scores, and tumor purity per each sample
samples	vector of character strings specifying sample names to be plotted. Defaults to "all_samples", which creates plots for all input samples
platform	character string indicating platform type. Defaults to "affymetrix"
output.dir	character string specifying a directory where plots should be saved. Defaults to "estimated_purity_plots"

Details

This function produces scatterplots (as PNG files) for each requested sample; it plots tumor purity against ESTIMATE score. At present, only the Affymetrix platform is supported.

Author(s)

Kosuke Yoshihara [e-mail]

Examples

in.file <- system.file("extdata", "sample_purity.gct", package="estimate")
plotPurity(scores=in.file)

estimate documentation built on May 2, 2019, 4:38 p.m.