plot_peakGeneCor: plot_peakGeneCor

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

plot_peakGeneCor

Description

plot_peakGeneCor

Usage

plot_peakGeneCor(
  mmAnnoCor,
  select_gene,
  addLine = TRUE,
  addFullInfo = TRUE,
  sigShow = c("pvalue", "padj", "qvalue")
)

Arguments

mmAnnoCor	the annotated GRange object from peakGeneCor or enhancerPromoterCor
select_gene	a gene_id which you want to show
addLine	whether add cor line
addFullInfo	whether add full feature info on plot
sigShow	one of 'pvalue' 'padj' 'qvalue'

Value

ggplot2 object

Examples

if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
    data("RNA_normCount")
    data("ATAC_normCount")
    Txdb <- TxDb.Athaliana.BioMart.plantsmart28
    seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
    peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
    peak_GR <- loadPeakFile(peak_path)[1:100]
    mmAnno <- mm_geneScan(peak_GR, Txdb)

    ATAC_colData <- data.frame(
        row.names = colnames(ATAC_normCount),
        type = gsub("_R[0-9]", "", colnames(ATAC_normCount))
    )

    integrate_replicates(ATAC_normCount, ATAC_colData) -> ATAC_normCount_merge
    RNA_colData <- data.frame(
        row.names = colnames(RNA_normCount),
        type = gsub("_R[0-9]", "", colnames(RNA_normCount))
    )
    integrate_replicates(RNA_normCount, RNA_colData) -> RNA_normCount_merge
    mmAnnoCor <- peakGeneCor(
        mmAnno = mmAnno,
        peakScoreMt = ATAC_normCount_merge,
        geneScoreMt = RNA_normCount_merge,
        parallel = FALSE
    )

    plot_peakGeneCor(mmAnnoCor, select_gene = "AT5G01010")

}

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.