term_gene_heatmap: Create Terms by Genes Heatmap

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Create Terms by Genes Heatmap

Description

Create Terms by Genes Heatmap

Usage

term_gene_heatmap(
  result_df,
  genes_df,
  num_terms = 10,
  use_description = FALSE,
  low = "red",
  mid = "black",
  high = "green",
  legend_title = "change",
  sort_terms_by_p = FALSE,
  ...
)

Arguments

result_df	A dataframe of pathfindR results that must contain the following columns: Term_Description Description of the enriched term (necessary if use_description = TRUE) ID ID of the enriched term (necessary if use_description = FALSE) lowest_p the highest adjusted-p value of the given term over all iterations Up_regulated the up-regulated genes in the input involved in the given term's gene set, comma-separated Down_regulated the down-regulated genes in the input involved in the given term's gene set, comma-separated
genes_df	the input data that was used with run_pathfindR. It must be a data frame with 3 columns: Gene Symbol (Gene Symbol) Change value, e.g. log(fold change) (optional) p value, e.g. adjusted p value associated with differential expression The change values in this data frame are used to color the affected genes
num_terms	Number of top enriched terms to use while creating the plot. Set to NULL to use all enriched terms (default = 10)
use_description	Boolean argument to indicate whether term descriptions (in the 'Term_Description' column) should be used. (default = FALSE)
low	a string indicating the color of 'low' values in the coloring gradient (default = 'green')
mid	a string indicating the color of 'mid' values in the coloring gradient (default = 'black')
high	a string indicating the color of 'high' values in the coloring gradient (default = 'red')
legend_title	legend title (defaut = 'change')
sort_terms_by_p	boolean to indicate whether to sort terms by 'lowest_p' (TRUE) or by number of genes (FALSE) (default = FALSE)
...	additional arguments for input_processing (used if genes_df is provided)

Value

a ggplot2 object of a heatmap where rows are enriched terms and columns are involved input genes. If genes_df is provided, colors of the tiles indicate the change values.

Examples

term_gene_heatmap(example_pathfindR_output, num_terms = 3)

pathfindR documentation built on Oct. 9, 2023, 1:07 a.m.