circos_heatmap: Write tiles of arbitrary heat-mappable data in circos.
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

circos_heatmap

R Documentation

Write tiles of arbitrary heat-mappable data in circos.

Description

This function tries to make the writing circos heatmaps 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_heatmap.txt It then writes out a configuration plot stanza in circos/conf/bob_heatmap.conf and finally adds an include to circos/bob.conf

Usage

circos_heatmap(
  cfg,
  input,
  tablename = NULL,
  colname = "logFC",
  color_mapping = 0,
  min_value = NULL,
  max_value = NULL,
  basename = "",
  colors = NULL,
  color_choice = "spectral-9-div",
  scale_log_base = 1,
  outer = 0.9,
  rules = NULL,
  width = 0.08,
  spacing = 0.02
)

Arguments

`cfg`	Result of circos_prefix(), contains a bunch of useful material.
`input`	Dataframe with starts/ends and the floating point information.
`tablename`	Provide a name for the input table in case it is coming from a combine_de_tables result.
`colname`	Name of the column with the data of interest.
`color_mapping`	0 means no overflows for min/max, 1 means overflows of min get a chosen color, 2 means overflows of both min/max get chosen colors.
`min_value`	Minimum value for the data.
`max_value`	Maximum value for the data.
`basename`	Make sure the written configuration files get different names with this.
`colors`	Colors of the heat map.
`color_choice`	Name of the heatmap to use, I forget how this interacts with color...
`scale_log_base`	Defines how the range of colors will be ranged with respect to the values in the data.
`outer`	Floating point radius of the circle into which to place the heatmap.
`rules`	some extra rules?
`width`	Width of each tile in the heatmap.
`spacing`	Radial distance between outer, inner, and inner to whatever follows.