Plot Gain or Loss of cytobands of the most variables cytobands

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

Examples


data("scExp")
scExp = calculate_CNA(scExp,  control_samples = unique(scExp$sample_id)[1],
ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
#> Warning: One of the cytoBand has no reads in control. Empty control cytobands logRatios are set to 1.
plot_gain_or_loss_barplots(scExp, cells = scExp$cell_id[which(
scExp$sample_id %in% unique(scExp$sample_id)[2])])


data("scExp")
scExp = calculate_CNA(scExp,  control_samples = unique(scExp$sample_id)[1],
ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
#> Warning: One of the cytoBand has no reads in control. Empty control cytobands logRatios are set to 1.
plot_gain_or_loss_barplots(scExp, cells = scExp$cell_id[which(
scExp$sample_id %in% unique(scExp$sample_id)[2])])