plotScatterPairs: Scatter plot of all pairs of variables stratified by test...

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Scatter plot of all pairs of variables stratified by test variable

Description

Scatter plot of all pairs of variables stratified by test variable

Usage

plotScatterPairs(epiSignal, peakIDs, testVariable, size = 1)

Arguments

epiSignal	matrix or EList of epigentic signal. Rows are features and columns are samples
peakIDs	feature names to extract from rows of epiSignal
testVariable	factor indicating two subsets of the samples to compare
size	size of points

Value

ggplot2 of combined pairwise scatter plots

Examples

library(GenomicRanges)

data('decorateData')

# Evaluate hierarchical clsutering
treeList = runOrderedClusteringGenome( simData, simLocation ) 

# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList, method = "meanClusterSize", meanClusterSize=c(10, 30) )

# get peak ID's from chr1, cluster 1
peakIDs = getFeaturesInCluster( treeListClusters, "chr20", 2, "30")

# plot comparison of correlation matrices for peaks in peakIDs
#  where data is subset by metadata$Disease
plotScatterPairs( simData, peakIDs, metadata$Disease) + ggtitle("chr20: cluster 1")

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.