tmodTagcloud: Tag cloud based on tmod results

Description Usage Arguments Details Value Examples

View source: R/multivariate.R

Description

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

Usage

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tmodTagcloud(results, filter = TRUE, simplify = TRUE,
  tag.col = "Title", weights.col = "auto", pval.col = "P.Value", ...)

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

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

...

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

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data(tmod)
fg <- tmod$MODULES2GENES[["LI.M127"]]
bg <- tmod$GENES$ID
result <- tmodHGtest( fg, bg )
tmodTagcloud(result)

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
NULL

tmod documentation built on Nov. 30, 2018, 4:19 p.m.