plot_enrichment_results: plot_enrichment_results

In langholee/XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Description

Plot GO and KEGG enrichment results

Usage

plot_enrichment_results(enriched_results,
  term_description = "term_description", sig_score = "pvalue",
  num_terms = 0, get_log = TRUE, fill_color = "darkgray")

Arguments

enriched_results	GO or KEGG enrichment results. See xina_enrichment and xina_enrichment
term_description	Description of terms to be drawn on Y axis. Default is "term_description" of XINA enrichment results.
sig_score	significant score to plot on X axis. Default is "pvalue".
num_terms	The number of terms to be plotted. Default is 0, which menas no limit.
get_log	If this is TRUE, 'plot_enrichment_results' will take -log10 of p-values.
fill_color	Default is 'darkgray'. You can change color of bars.

Value

ggplot bar graph

Examples

## Not run: 
library(STRINGdb)

# load XINA example data
data(xina_example)

# Get STRING database for protein-protein intereaction information
string_db <- STRINGdb$new( version="10", species=9606,
score_threshold=0, input_directory="" )
string_db

# XINA analysis with STRING DB
xina_result <- xina_analysis(example_clusters, string_db)

# Select proteins that showed cluster #1 in the Stimulus2 condition
subgroup <- subset(example_clusters$aligned, Stimulus2==1)
protein_list <- as.vector(subgroup$`Gene name`)

# Enrichment test and get significantly enriched functional terms
# that have adjuseted p-value less than 0.1
kegg_enriched <- xina_enrichment(string_db, protein_list,
enrichment_type = "KEGG", pval_threshold=0.1)
plot_enrichment_results(kegg_enriched$KEGG, num_terms=10)

## End(Not run)

langholee/XINA documentation built on March 17, 2020, 5:23 p.m.