plot_reduced_dim_scExp_CNA {ChromSCape} | R Documentation

## Plot UMAP colored by Gain or Loss of cytobands

### Description

Plot UMAP colored by Gain or Loss of cytobands

### Usage

    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$sample_id)[1],
    ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
    plot_reduced_dim_scExp_CNA(scExp, get_most_variable_cyto(scExp)$cytoBand[1])

[Package ChromSCape version 1.2.62 Index]