plot_peakGeneAlias_summary: plot_peakGeneAlias_summary

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

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)

}

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