plotsynexprs {attract} | R Documentation

## Visualizing the Average Expression Profile of a Synexpression Group.

### 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])
     }

[Package attract version 1.46.0 Index]