nem (version 2.46.0)

plotEffects: Plots data according to a phenotypic hierarchy

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'

Value

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

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.

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)