TOMplot: Graphical representation of the Topological Overlap Matrix

In WGCNA: Weighted Correlation Network Analysis

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

See Also

heatmap, the workhorse function doing the plotting.

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.