plot_peakGeneCor {FindIT2} | R Documentation

## 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")

    }

[Package FindIT2 version 1.0.3 Index]