WGCNA: TOMplot – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

TOMplot

Graphical representation of the Topological Overlap Matrix

Description

Graphical representation of the Topological Overlap Matrix using a heatmap plot combined with the corresponding hierarchical clustering dendrogram and module colors.

Usage

TOMplot(
   dissim, 
   dendro, 
   Colors = NULL, 
   ColorsLeft = Colors, 
   terrainColors = FALSE, 
   setLayout = TRUE,
   ...)

Arguments

`dissim`	a matrix containing the topological overlap-based dissimilarity
`dendro`	the corresponding hierarchical clustering dendrogram
`Colors`	optional specification of module colors to be plotted on top
`ColorsLeft`	optional specification of module colors on the left side. If `NULL`, `Colors` will be used.
`terrainColors`	logical: should terrain colors be used?
`setLayout`	logical: should layout be set? If `TRUE`, standard layout for one plot will be used. Note that this precludes multiple plots on one page. If `FALSE`, the user is responsible for setting the correct layout.
`...`	other graphical parameters to `heatmap`.

Details

The standard heatmap function uses the layout function to set the following layout (when Colors is given):

0 0 5
0 0 2
4 1 3

To get a meaningful heatmap plot, user-set layout must respect this geometry.

Value

None.

Author(s)

Steve Horvath and Peter Langfelder