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Plot diversity distributions (density) by sample type

Source: R/generate_plots.R
plot_diversity_density.Rd

Plot diversity distributions (density) by sample type

Usage

plot_diversity_density(se, assay_name = "diversity", sample_type_col = NULL)

Arguments

se

A `SummarizedExperiment` returned by `calculate_diversity`.

assay_name

Name of the assay to use (default: "diversity").

sample_type_col

Optional column name in `colData(se)` with sample types. If missing, sample types are inferred from column names (suffix after the last underscore) or set to 'Group'.

Value

A `ggplot` object with layered density plots.

Examples

data("tcga_brca_luma", package = "TSENAT")
rc <- as.matrix(tcga_brca_luma[1:100, -1, drop = FALSE])
gs <- tcga_brca_luma[1:100, 1]
se <- calculate_diversity(rc, gs, q = 0.1, norm = FALSE)
# Manually set sample_type in colData for plotting
SummarizedExperiment::colData(se)$sample_type <- 
  factor(gsub(".*_", "", colnames(rc)))
plot_diversity_density(se)