TOMplot: Graphical representation of the Topological Overlap Matrix

Description Usage Arguments Details Value Author(s) See Also

Description

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

Usage

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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):

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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.



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