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

Description Usage Arguments Value Examples

View source: R/plotCorrPairs.R

Description

Scatter plot of all pairs of variables stratified by test variable

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
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 Aug. 8, 2019, 1:48 p.m.