plotsynexprs: Visualizing the Average Expression Profile of a Synexpression...

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

This function plots the average expression profile for a specific synexpression group.

Usage

		plotsynexprs(mySynExpressionSet, tickMarks, tickLabels, vertLines, index=1, ...)

Arguments

mySynExpressionSet	SynExpressionSet object.
tickMarks	numeric vector of specifying the location of the tick marks along the x-axis. There should be one tick for each cell type or group.
tickLabels	character vector specifying the labels to be appear underneath the tick marks on the x-axis. These should correspond to the cell type or group names.
vertLines	numeric vector specifying the location of the vertical lines that indicate the cell type or group-specific regions along the x-axis.
index	numeric value specifying which synexpression group should be plotted.
...	additional arguments.

Details

Generic plotting parameters can be passed to this function to create a more sophisticated plot, e.g col="blue", main="Synexpression Group 1".

Value

A plot showing the average expression profile for the synexpression group specified.

Author(s)

Jessica Mar

Examples

data(subset.loring.eset)
attractor.states <- findAttractors(subset.loring.eset, "celltype", nperm=10, annotation="illuminaHumanv1.db")
remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
mapk.syn <- findSynexprs("04010", attractor.states, remove.these.genes)
par(mfrow=c(2,2)) 
pretty.col <- rainbow(3) 
for( i in 1:3 ){
	plotsynexprs(mapk.syn, tickMarks=c(6, 28, 47, 60), tickLabels=c("ESC", "PRO", "NSC", "TER"), vertLines=c(12.5, 43.5, 51.5), index=i, 
			main=paste("Synexpression Group ", i, sep=""), col=pretty.col[i])
 }

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.