Plot UMAP colored by Gain or Loss of cytobands

plot_reduced_dim_scExp_CNA(scExp, cytoBand)

Arguments

scExp	A SingleCellExperiment with "gainOrLoss_cytoBand" reducedDim slot filled. See `calculate_gain_or_loss`
cytoBand	Which cytoBand to color cells by

Value

Plot the gains/lost of the cytoband overlayed on the epigenetic UMAP.

Examples


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