plot_reduced_dim_scExp_CNA: Plot UMAP colored by Gain or Loss of cytobands
In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App
plot_reduced_dim_scExp_CNA 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])
vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.
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| plot_reduced_dim_scExp_CNA | 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 |
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])
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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