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Plot median +- IQR of Tsallis entropy across q values by group

Source: R/generate_plots.R
plot_tsallis_q_curve.Rd

This reproduces the `tsallis-q-curve-mean-sd` plot from the vignette: for each q value, compute per-gene Tsallis entropy per sample, summarize across genes by group (median and IQR) and plot median with a ribbon spanning median +- IQR/2.

Usage

plot_tsallis_q_curve(
  se,
  assay_name = "diversity",
  sample_type_col = "sample_type"
)

Arguments

se

A `SummarizedExperiment` returned by `calculate_diversity`.

assay_name

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

sample_type_col

Column name in `colData(se)` containing sample type labels (default: "sample_type").

Value

A `ggplot` object showing median +- IQR across q values by group.

Examples

data("tcga_brca_luma", package = "TSENAT")
rc <- as.matrix(tcga_brca_luma[1:40, -1, drop = FALSE])
gs <- tcga_brca_luma[1:40, 1]
se <- calculate_diversity(rc, gs,
    q = seq(0.01, 0.1, by = 0.03), norm = FALSE
)
p <- plot_tsallis_q_curve(se)
p