plotMotif: Correlation Motif plot

In kennethabarr/CormotifCounts: Correlation Motif Fit

Correlation Motif plot

Description

This function plots the Correlation Motif patterns and the associated prior probability distributions.

Usage

plotMotif(fitted_cormotif,title="")

Arguments

fitted_cormotif	The object obtained from cormotiffit.
title	The title for the graph.

Details

Each row in both graphs corresponds to one motif pattern. The left graph shows the correlation motif pattern. The grey color scale of cell (k,d) indicates the probability that motif k is differentially expressed in study d. Each row of the bar chart corresponds to the motif pattern in the same row of the left pattern graph. The length of the bar in the bar chart shows the number of genes of the given pattern in the dataset, which is equal to motif.fitted\$bestmotif\$motif.prior multiplying the number of total genes.

Author(s)

Hongkai Ji, Yingying Wei

References

Ji, H., Wei, Y.,(2011) Correlation Motif. Unpublished

Examples

data(simudata2)
n<-nrow(simudata2)
m<-ncol(simudata2)
#the expression data is from the second column to m
exprs.simu2<-as.matrix(simudata2[,2:m])

#prepare the group ID number for each sample array
data(simu2_groupid)

#prepare the design matrix for each group of samples
data(simu2_compgroup)

#fit 2 correlation motif to the data
motif.fitted<-cormotiffit(exprs.simu2, simu2_groupid,simu2_compgroup,K=2)

plotMotif(motif.fitted)

kennethabarr/CormotifCounts documentation built on Sept. 6, 2024, 11:57 a.m.