plotCorAcrossRef: Function to plot correlation across genome

In kokonech/InTAD: Search for correlation between epigenetic signals and gene expression in TADs

Description

This function creates a plot of correlation strength in target genomic region from the result table. The X-coordinates represent signals, Y-coords represent genes, while each dot represents -log10(P-value) from correlation test. Additionallly all TAD boundaries can be visualized.

Usage

plotCorAcrossRef(obj, corRes, targetRegion, showCorVals = FALSE,
  symmetric = FALSE, tads = NULL)

Arguments

obj	InTADSig object with signals and genes combined in TADS
corRes	Correlation result table created by function findCorrelation()
targetRegion	Target genomic region visualise.
showCorVals	Use this option to visualize postive correlation values instead of correlation strength
symmetric	Activate mirrow symmetry for gene-signal connections
tads	TAD regions to visualize. By default only TADs persent in correlation result table are applied (NULL value).

Value

A ggplot object for visualization or customization.

Examples

inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)
inTadSig <- combineInTAD(inTadSig, tadGR)
corData <- findCorrelation(inTadSig, method="pearson")
plotCorAcrossRef(inTadSig,corData,GRanges("chr15:25000000-28000000"))

kokonech/InTAD documentation built on Jan. 1, 2021, 9:23 p.m.