chip_summary: TF ChIPseq data summary plots

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This method generates various summary plots for TF ChIPseq data.

• A table summarizing quantils of peak enrichment, p-value and q-value

• A distribution beeswarm plot for peak enrichment values.

• A distribution beeswarm plot for peak p-value.

• A distribution beeswarm plot for peak width.

• A pie chart showing peak annotation distribution.

If there is no peak information, it returns blank plot with "No Data" text

Usage

chip_summary(
  sampleId,
  peakAnnotation,
  peakFile,
  peakFormat,
  pval_cutoff = 20,
  enrichment_cutoff = 3,
  markTargets = NULL,
  pointColor = NULL,
  pointAlpha = NULL
)

Arguments

sampleId	sampleId
peakAnnotation	macs2 peak annotation file generated by narrowPeak_annotate()
peakFile	narrowPeak or broadPeak file generated by macs2
peakFormat	One of narrowPeak or broadPeak
pval_cutoff	A cutoff for -log10(p-value) for drawing horizontal line in beeswarm plot. Default: 20
enrichment_cutoff	A cutoff for peak enrichment for drawing horizontal line in beeswarm plot. Default: 3
markTargets	A named list of target genes which needs to be annotated in the scatter plot. Default: NULL
pointColor	A named vector with colors for each target category in markTargets list. Default: NULL
pointAlpha	A named vector of alpha vlues for each target category in markTargets list. Default: NULL

Value

A list with following elements is returned.

• data: plot data used for plotting

• figure: A combined figure generated by ggpubr::ggarrange

• plots: Individual ggplot list for each plot.

  • table: a ggtable object for quantile stats

  • distribution: A list with two beeswarm plot objects: enrichment, pval.

  • annoPie: A pie chart for peak annotation distribution

Examples

NA

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.