Create Terms by Genes Heatmap

Source: R/visualization.R

Create Terms by Genes Heatmap

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:

  1. Gene Symbol (Gene Symbol)

  2. Change value, e.g. log(fold change) (optional)

  3. 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 (default = '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)