UpSet_plot: Create UpSet Plot of Enriched Terms

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Create UpSet Plot of Enriched Terms

Description

Create UpSet Plot of Enriched Terms

Usage

UpSet_plot(
  result_df,
  genes_df,
  num_terms = 10,
  method = "heatmap",
  use_description = FALSE,
  low = "red",
  mid = "black",
  high = "green",
  ...
)

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)
method	the option for producing the plot. Options include 'heatmap', 'boxplot' and 'barplot'. (default = 'heatmap')
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')
...	additional arguments for input_processing (used if genes_df is provided)

Value

UpSet plots are plots of the intersections of sets as a matrix. This function creates a ggplot object of an UpSet plot where the x-axis is the UpSet plot of intersections of enriched terms. By default (i.e. method = 'heatmap') the main plot is a heatmap of genes at the corresponding intersections, colored by up/down regulation (if genes_df is provided, colored by change values). If method = 'barplot', the main plot is bar plots of the number of genes at the corresponding intersections. Finally, if method = 'boxplot' and if genes_df is provided, then the main plot displays the boxplots of change values of the genes at the corresponding intersections.

Examples

UpSet_plot(example_pathfindR_output)

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