Plot q-curve profile for a single gene comparing groups — plot_tsallis_gene

For a selected gene, plot per-sample Tsallis entropy across q values and overlay per-group median +/- IQR ribbons so group-level differences are easy to compare. Expects a `SummarizedExperiment` produced by `calculate_diversity()` with `_q=` suffixes in column names.

Usage

plot_tsallis_gene_profile(
  se,
  gene = NULL,
  lm_res = NULL,
  n_top = 10,
  assay_name = "diversity",
  sample_type_col = "sample_type",
  show_samples = FALSE
)

Arguments

se: A `SummarizedExperiment` from `calculate_diversity()`.
gene: Character scalar or vector; gene symbol(s) to plot. If NULL and `lm_res` is supplied, the top `n_top` genes from `lm_res` (by `adj_p_interaction` or `p_interaction`) are used.
lm_res: Optional data.frame result from `calculate_lm_interaction()`. When supplied and `gene` is NULL, the top `n_top` significant genes will be plotted.
n_top: Number of top genes to plot when `lm_res` is provided (default: 10).
assay_name: Name of the assay to use (default: "diversity").
sample_type_col: Column name in `colData(se)` with sample type labels (default: "sample_type"). If missing, a single-group fallback is used.
show_samples: Logical; if TRUE, draw per-sample lines in the background (default: FALSE).

Value

A `ggplot` object when a single gene is requested, or a named list of `ggplot` objects when multiple genes are requested.

Examples

mat <- matrix(runif(8), nrow = 2, dimnames = list(c("g1", "g2"), c("s1_q=0.1", "s1_q=1", "s2_q=0.1", "s2_q=1")))
se <- SummarizedExperiment::SummarizedExperiment(assays = list(diversity = mat))
plot_tsallis_gene_profile(se, gene = "g1")