plot_peakGeneAlias_summary {FindIT2} | R Documentation

## plot_peakGeneAlias_summary

### Description

plot_peakGeneAlias_summary

### Usage

    plot_peakGeneAlias_summary(
      mmAnno,
      mmAnno_corFilter = NULL,
      output_type = c("gene_id", "feature_id"),
      fillColor = "#ca6b67"
    )

### Arguments

`mmAnno` | the annotated GRange object from mm_geneScan or mm_nearestGene
`mmAnno_corFilter` | the filter mmAnno object according to p-value or cor, defalut is NULL
`output_type` | one of 'gene_id' or 'feature_id'
`fillColor` | the bar plot color

### Value

a ggplot object

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
        Txdb <- TxDb.Athaliana.BioMart.plantsmart28
        seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))

        peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
        peak_GR <- loadPeakFile(peak_path)
        peakAnno <- mm_nearestGene(peak_GR, Txdb)

        plot_peakGeneAlias_summary(peakAnno)

    }

[Package FindIT2 version 1.0.3 Index]