modCorPlot

Plot a correlation heatmap for modules

Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis. See Zyla et al (2019)
<doi:10.1093/bioinformatics/btz447>.

January Weiner

tmod

Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics

modCorPlot function

<dl><dt>modules</dt>
<dd>either a character vector with module IDs from mset, or a list which
contains the module members</dd>
<dt>mset</dt>
<dd>Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)</dd>
<dt>heatmap_func</dt>
<dd>function drawing the heatmap</dd>
<dt>labels</dt>
<dd>Labels for the modules (if NULL, labels will be retrieved from `mset`)</dd>
<dt>stat</dt>
<dd>Type of statistics to return. 
"jaccard": Jaccard index (default);
"number": number of common genes;
"soerensen": Soerensen-Dice coefficient;
"overlap": Szymkiewicz-Simpson coefficient.</dd>
<dt>upper.cutoff</dt>
<dd>Specify upper cutoff for the color palette</dd>
<dt>...</dt>
<dd>Any further parameters are passed to the heatmap function (by
default, [pheatmap()].</dd></dl>

Arguments

Plot a correlation heatmap for modules — modCorPlot

<dl>

<dt>modules</dt>
<dd>either a character vector with module IDs from mset, or a list which
contains the module members</dd>


<dt>mset</dt>
<dd>Which module set to use. Either a character vector ("LI", "DC" or "all", default: all) or an object of class tmod (see "Custom module definitions" below)</dd>


<dt>heatmap_func</dt>
<dd>function drawing the heatmap</dd>


<dt>labels</dt>
<dd>Labels for the modules (if NULL, labels will be retrieved from `mset`)</dd>


<dt>stat</dt>
<dd>Type of statistics to return. 
"jaccard": Jaccard index (default);
"number": number of common genes;
"soerensen": Soerensen-Dice coefficient;
"overlap": Szymkiewicz-Simpson coefficient.</dd>


<dt>upper.cutoff</dt>
<dd>Specify upper cutoff for the color palette</dd>


<dt>...</dt>
<dd>Any further parameters are passed to the heatmap function (by
default, [pheatmap()].</dd>

</dl>

modCorPlot: Plot a correlation heatmap for modules

Description

Usage

Value

Arguments