circos_hist: Write histograms of arbitrary floating point data in circos.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Write histograms of arbitrary floating point data in circos.

Description

This function tries to make the writing of histogram data in circos easier. Like circos_plus_minus() it works in 3 stages, It writes out a data file using cfgout as a basename and the data from df in the circos histogram format into circos/data/bob_hist.txt It then writes out a configuration plot stanza in circos/conf/bob_hist.conf and finally adds an include to circos/bob.conf

Usage

circos_hist(
  cfg,
  input,
  tablename = NULL,
  annot_source = "cfg",
  colname = "logFC",
  basename = "",
  color = "blue",
  fill_color = "blue",
  fill_under = "yes",
  extend_bin = "no",
  thickness = "0",
  orientation = "out",
  outer = 0.9,
  width = 0.08,
  spacing = 0
)

Arguments

cfg	Result of circos_prefix(), contains a bunch of useful material.
input	Dataframe or table with starts/ends and the floating point information.
tablename	A likely input for this is a combine_de_tables() result, if so, provide the table's name here.
annot_source	This parameter was added to make it possible to add an arbitrary dataframe of other annotation information.
colname	Name of the column with the data of interest.
basename	Location to write the circos data (usually cwd).
color	Color of the plotted data.
fill_color	Guess
fill_under	The circos histogram fill under parameter
extend_bin	Extend bins?
thickness	histogram thickness.
orientation	facing in or out?
outer	Floating point radius of the circle into which to place the data.
width	Radial width of each tile.
spacing	Distance between outer, inner, and inner to whatever follows.

Value

Radius after adding the histogram and the spacing.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.