giDensityPlot: Genomic instability plot

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

Genomic instability plot

Description

This function plot the genomic instability distribution, gaussian fits and null distribution if available

Usage

giDensityPlot(inferCNV, legend = c("topleft", "top", "topright", "none"), ...)

Arguments

inferCNV	Object of class inferCNV
legend	Character string indicating the location of the legend. none to not include it
...	Additional parameters for plot()

Value

None, a figure is created in the default output device

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)
giDensityPlot(cnv)

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