plot.effects {nem}R Documentation

Plots data according to a phenotypic hierarchy

Description

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

Usage

plot.effects(x,nem,border=TRUE,...)

Arguments

x data matrix
nem phenotypic hierarchy (object of class 'score' or 'pairwise')
border draw red lines to indicate gene-specific effect reporters. Default: TRUE
... additional parameters for the plotting function

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.

Author(s)

Florian Markowetz <URL: http://genomics.princeton.edu/~florian>

Examples

   data("BoutrosRNAi2002")
   D <- BoutrosRNAiDiscrete[,9:16]
   res <- nem(D,para=c(.13,.05))
   plot.effects(D,res)

[Package nem version 2.2.1 Index]