plot.inferCNV: Plot chromosome map

In reef103/genomicInstability: Genomic Instability estimation for scRNA-Seq

Plot chromosome map

Description

This function generates a chromosomes map plot for the inferred CNVs

Usage

## S3 method for class 'inferCNV'
plot(x, output = NULL, threshold = 0.2, gamma = 1.5, resolution = 150, ...)

Arguments

x	Object of class inferCNV
output	Optional output PDF file name (with extension)
threshold	Likelihood threshold for identifying genomically inestable cells/samples, 0 disables this filter
gamma	Number indicating the gamma transformation for the colors
resolution	Integer indicating the ppi for the png and jpg output files
...	Additional parameters for plot

Value

Nothing, a plot is generated in the default output devise

See Also

[giLikelihood()] to estimate the relative likelihood, [genomicInstabilityScore()] to estimate the genomic instability score for each cell in the dataset, and [inferCNV()] to infer the enrichment of loci-blocks in the gene expression data.

Examples

eh <- ExperimentHub::ExperimentHub()
dset <- eh[["EH5419"]]
tpm_matrix <- SummarizedExperiment::assays(dset)$TPM
set.seed(1)
tpm_matrix <- tpm_matrix[, sample(ncol(tpm_matrix), 500)]
cnv <- inferCNV(tpm_matrix)
cnv <- genomicInstabilityScore(cnv)
cnv <- giLikelihood(cnv, distros=c(3, 3), tumor=2:3)
plot(cnv, output='test.png')

reef103/genomicInstability documentation built on Oct. 10, 2022, 12:33 a.m.