circos_tile: Write tiles of arbitrary categorical point data in circos.

View source: R/plot_circos.R

circos_tileR Documentation

Write tiles of arbitrary categorical point data in circos.

Description

This function tries to make the writing circos tiles easier. Like circos_plus_minus() and circos_hist() 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_tile.txt It then writes out a configuration plot stanza in circos/conf/bob_tile.conf and finally adds an include to circos/bob.conf

Usage

circos_tile(
  cfg,
  df,
  colname = "logFC",
  basename = "",
  colors = NULL,
  thickness = 80,
  padding = 1,
  margin = 0,
  stroke_thickness = 0,
  orientation = "out",
  outer = 0.9,
  width = 0.08,
  spacing = 0
)

Arguments

cfg

Result from circos_prefix().

df

Dataframe with starts/ends and the floating point information.

colname

Name of the column with the data of interest. chromosome)

basename

Used to make unique filenames for the data/conf files.

colors

Colors of the data.

thickness

How thick to make the tiles in radial units.

padding

Space between tiles.

margin

How much space between other rings and the tiles?

stroke_thickness

Size of the tile outlines.

orientation

Facing in or out.

outer

Floating point radius of the circle into which to place the categorical data.

width

Width of each tile.

spacing

Radial 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.