plotPurity: plotPurity

In IOBR: Immune Oncology Biological Research

plotPurity

Description

This function generates scatterplots of tumor purity based on ESTIMATE scores for given samples.

Usage

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

Arguments

scores	A character string specifying the path to the input file containing ESTIMATE scores. The file should be a tab-separated table with appropriate headers.
samples	A character vector specifying the sample names to plot. The default is "all_samples", which plots all samples in the input file.
platform	A character string specifying the platform used for data collection. Can be "affymetrix", "agilent", or "illumina". Currently, only "affymetrix" is implemented.
output.dir	A character string specifying the directory to save the output plots. If 'NULL', plots are not saved. Default is 'NULL'.

Value

No return value. The function generates and saves scatterplots in the specified output directory.

Examples

# Create a sample ESTIMATE score matrix
scores_data <- data.frame(
  Sample1 = c(100, 200, 500, 0.80),
  Sample2 = c(120, 220, 450, 0.70),
  Sample3 = c(140, 240, 600, 0.90),
  row.names = c(
    "StromalScore", "ImmuneScore", "ESTIMATEScore",
    "TumorPurity"
  ),
  check.names = FALSE
)

# Write to a temporary GCT file
scores_file <- tempfile(fileext = ".gct")
outputGCT(scores_data, scores_file)

IOBR documentation built on May 30, 2026, 5:07 p.m.