get_chip_signal_heatmap: Generate a ChIP signal heatmap for a given sample. #'...

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Generate a ChIP signal heatmap for a given sample. #' @description This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot will be plotted as an output of EnrichedHeatmap::normalizeToMatrix().

Description

Generate a ChIP signal heatmap for a given sample. #' @description This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot will be plotted as an output of EnrichedHeatmap::normalizeToMatrix().

Usage

get_chip_signal_heatmap(
  path_to_bw_file,
  target_region,
  extend = 5000,
  background = NA,
  mean_mode = "w0",
  w = 50,
  smooth = TRUE,
  target_ratio = 0,
  name = NULL,
  col = NULL,
  column_title = NULL,
  axis_name = NULL,
  top_annotation = NULL,
  ...
)

Arguments

path_to_bw_file	a character string denoting a path to a bw file. String can be an absolute path or the valid URL pointing to bw file.
target_region	an object of the class GenomicRanges. Singal will be plotted against this regions.
extend	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
background	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
mean_mode	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
w	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
smooth	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
target_ratio	pass to the same argument of EnrichedHeatmap::normalizeToMatrix().
name	pass to the same argument of EnrichedHeatmap::EnrichedHeatmap().
col	pass to the same argument of EnrichedHeatmap::EnrichedHeatmap().
column_title	pass to the same argument of EnrichedHeatmap::EnrichedHeatmap().
axis_name	pass to the same argument of EnrichedHeatmap::EnrichedHeatmap().
top_annotation	pass to the same argument of EnrichedHeatmap::EnrichedHeatmap().
...	Other arguments pass to EnrichedHeatmap::EnrichedHeatmap().

Details

To obtain the order of targets from the output heatmap the suggested approach is ⁠hm = ComplexHeatmap::draw(hm); ComplexHeatmap::row_order(hm)⁠.

Value

an output of the function EnrichedHeatmap::EnrichedHeatmap().

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.