PathWC: Make a Word Cloud of enriched pathway terms

In kevincjnixon/BinfTools: Useful functions for standard analyses

Make a Word Cloud of enriched pathway terms

Description

Use the textmining and wordcloud packages to make a word cloud. Great for using with enriched GO/GSEA term names

Usage

PathWC(
  text,
  cols = "Dark2",
  retTerms = FALSE,
  minfreq = 3,
  rmwords = c("regulation", "process", "positive", "negative", "mediated", "cell",
    "cellular", "protein"),
  title = ""
)

Arguments

text	Character vector of terms to be processed for a word cloud
cols	Colour palette. Can be RColourBrewer palette name, rgb, colour names, or hexadecimal. Default is "Dark2"
retTerms	Boolean if term-document matrix dataframe should be returned. Default=FALSE
minfreq	Minimum frequency for a word to be included in the word cloud. Default=3
rmwords	Character vector of words to be filtered out (in addition to the default english stop words and words shorter than 3 letters) - defaults to c("regulation","process","positive","negative","mediated", "cell","cellular", "protein")
title	Character indicating title of word cloud. Defaults to blank "".

Value

A Word cloud showing most frequent words in input text, and if indicated, a data frame of word frequencies.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.