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 = "estimated_purity_plots"
)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. The default is "estimated_purity_plots".
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)