tmod (version 0.50.13)

tmodTagcloud: 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,
  ...
)

Value

Either NULL or whatever tagcloud returns

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.

Examples

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