plotEffects: Plots data according to a phenotypic hierarchy

In cbg-ethz/pcNEM: Probabilistic combinatorial nested effects model

Description

plotEffects visualizes the subset structure in the data by reordering rows and columns according to the topological order given by a phenotypic hierarchy.

Usage

plotEffects(D,nem,border=TRUE,legend=TRUE,order=NULL,orderSCC=TRUE,palette="BlueRed",...)

Arguments

D	data matrix
nem	phenotypic hierarchy (object of class 'score' or 'pairwise')
border	draw red lines to indicate gene-specific effect reporters. Default: TRUE
legend	plot a legend. Default: TRUE
order	pre-define an order of the S-genes instead of the topological order to visualize the subset structure. Default: Use topological order.
orderSCC	Is the pre-defined order given on strongly connected components rather than on individual nodes?
palette	color palette to use: either 'BlueRed' (default) or 'Grey'
...	additional parameters for the graphics function 'image'

Details

The experiments in the columns are reordered according to the topological order given by a phenotypic hierarchy. The effect reporters in the rows are grouped together by their position in the hierarchy. The groups are then arranged by topological order. Within each group the rows are hierarchically clustered.

Value

ordering of the E-genes according to the hierarchy (vector of indices)

Note

This function was formerly named plot.effects. This naming is not possible any more, since S3 classes were used for the function plot.nem.

Author(s)

Florian Markowetz, Holger Froehlich

Examples

   data("BoutrosRNAi2002")
   D <- BoutrosRNAiDiscrete[,9:16]
   res <- nem(D,control=set.default.parameters(unique(colnames(D)), para=c(.13,.05)))
   if(require(Rgraphviz))
    plotEffects(D,res)

cbg-ethz/pcNEM documentation built on Sept. 27, 2019, 8:58 a.m.