sampleEnrichmentHeatmap: Draw a heatmap of enriched genesets in all samples

In sansomlab/gsfisher: Geneset Fisher

Draw a heatmap of enriched genesets in all samples

Description

Draw a heatmap of enriched genesets in all samples

Usage

sampleEnrichmentHeatmap(
  results_table,
  max_rows = 50,
  min_genes = 2,
  min_odds_ratio = 1.5,
  p_col = "p.val",
  adjust_pvalues = FALSE,
  padjust_method = "BH",
  pvalue_threshold = 0.1,
  maxl = 45,
  show_common = TRUE,
  sample_id_col = "cluster",
  sample_ids = NULL,
  title = "Enriched gene sets"
)

Arguments

results_table	A gofisher multi-sample results table.
max_rows	Maximum number of rows to show in the heatmap.
min_genes	Minimum number of genes to filter gene sets.
min_odds_ratio	Only genesets with odds ratios equal to or greater will be considered.
adjust_pvalues	Logical value indicating whether to adjust p-values across all sample.
padjust_method	Correction method. Can be abbreviated (see p.adjust.methods).
pvalue_threshold	P-value threshold.
maxl	Maximum length for gene set names (trimmed otherwise).
show_common	Logical value indicating whether to show gene sets enriched in all samples.
sample_id_col	The column of the results_table containing the sample id
sample_ids	A vector of sample identifiers to report. Can be used to subset the frame, or to add missing columns.
title	Title of the heat map plot.

Author(s)

Steve Sansom

See Also

readGMT p.adjust

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.