tmodTagcloud: Tag cloud based on tmod results

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Tag cloud based on tmod results

Description

Plot a tag (word) cloud based on results from tmod enrichment.

Usage

tmodTagcloud(
  results,
  filter = TRUE,
  simplify = TRUE,
  tag.col = "Title",
  min.auc = 0.5,
  max.qval = 0.05,
  plot = TRUE,
  weights.col = "auto",
  pval.col = "P.Value",
  maxn = NULL,
  ...
)

Arguments

results	data frame produced by one of the tmod enrichment tests
filter	Whether redundant and not annotated modules should be removed
simplify	Whether module names should be simplified
tag.col	Which column from results should be used as tags on the plot
min.auc	Minimal AUC to show (default: 0.5)
max.qval	Maximal adjusted p value to show (default: 0.05)
plot	Should the tag cloud be plotted or only returned
weights.col	Which column from results should be used as weights for the tag cloud
pval.col	Which column contains the P values which will be used to shade the tags
maxn	Maximum number of gene set enrichment terms shown on the plot (if NULL – default – all terms will be shown)
...	Any further parameters are passed to the tagcloud function

Details

The tags will be generated based on results from tmod or any other suitable data frame. The data frame must contain two numeric columns, specified with "weights.col" and "pval.col", which will be used to calculate the size and shade of the tags, respectively. Furthermore, it has to contain a column with tags (parameter "tag.col", by default "Title").

Any data frame can be used as long as it contains the specified columns.

Value

Either NULL or whatever tagcloud returns

Examples

data(tmod)
fg <- getModuleMembers("LI.M127")[[1]]
bg <- tmod$gv
result <- tmodHGtest( fg, bg )
tmodTagcloud(result)

tmod documentation built on March 31, 2023, 9 p.m.