circos_heatmap: Write tiles of arbitrary heat-mappable data in circos.

View source: R/plot_circos.R

circos_heatmapR 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.

Value

Radius after adding the histogram and the spacing.


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