plot_gain_or_loss_barplots: Plot Gain or Loss of cytobands of the most variables...

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Plot Gain or Loss of cytobands of the most variables cytobands

Description

Plot Gain or Loss of cytobands of the most variables cytobands

Plot Gain or Loss of cytobands of the most variables cytobands

Usage

plot_gain_or_loss_barplots(scExp, cells = NULL, top = 20)

plot_gain_or_loss_barplots(scExp, cells = NULL, top = 20)

Arguments

scExp	A SingleCellExperiment with "logRatio_cytoBand" reducedDim slot filled. See calculate_logRatio_CNA
cells	Cell IDs of the tumor samples to
top	Number of most variables cytobands to plot

Value

Plot the gains/lost in the selected cells of interest as multiple barplots

Plot the gains/lost in the selected cells of interest as multiple barplots

Examples

data("scExp")
scExp = calculate_CNA(scExp,  control_samples = unique(scExp$sample_id)[1],
ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
plot_gain_or_loss_barplots(scExp, cells = scExp$cell_id[which(
scExp$sample_id %in% unique(scExp$sample_id)[2])])


data("scExp")
scExp = calculate_CNA(scExp,  control_samples = unique(scExp$sample_id)[1],
ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
plot_gain_or_loss_barplots(scExp, cells = scExp$cell_id[which(
scExp$sample_id %in% unique(scExp$sample_id)[2])])

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.