chromosome_map: Create annotated chromosome map

In bailey-lab/miplicorn: A Framework for Molecular Inversion Probe and Amplicon Analysis

Create annotated chromosome map

Description

This function has been deprecated as it was a simple wrapper around plot_chromoMap() and plot_karyoploteR() and added unnecessary complexity to function calls.

Usage

chromosome_map(
  genome,
  probes,
  map_pkg = c("chromoMap", "karyoploteR"),
  title = "",
  colours = list(),
  ...
)

Arguments

genome	A tibble indicating the starting and ending position of each chromosome. Contains three columns: Name of the chromosome The starting position of the chromosome The ending position of the chromosome.
probes	A tibble indicating the starting and ending position of each probe. Contains four columns: Name of the chromosome the probe is on The starting position of the probe The ending position of the probe An identifier indicating the probe set the probe belongs to.
map_pkg	The package used for the underlying implementation of the chromosome map.
title	The title of the plot.
colours	A vector of colours indicating the annotation colour for each probe set.
...	<dynamic-dots> Additional arguments passed to internal plotting functions.

Details

Render a graphics visualization of entire chromosomes or chromosomal regions. Annotate multiple targeted regions to visualize probe targets.

Value

A chromoMap or karyoploteR object.

See Also

chromoMap::chromoMap() karyoploteR::plotKaryotype()

Examples

probes <- tibble::tribble(
  ~chrom, ~start, ~end, ~probe_set,
  "chr14", 2342135L, 2342284L, "IBC",
  "chr3", 830503L, 830769L, "DR2",
  "chr5", 482233L, 482391L, "IBC",
  "chr9", 375274L, 375417L, "IBC",
  "chr12", 532032L, 532281L, "DR2",
  "chr7", 383447L, 383653L, "HAP",
  "chr14", 1401991L, 1402160L, "IBC",
  "chr4", 734737L, 734936L, "HAP",
  "chr10", 93054L, 93223L, "IBC",
  "chr7", 162127L, 162277L, "IBC"
)

chromosome_map(genome_Pf3D7, probes, "chromoMap")
# ->
plot_chromoMap(genome_Pf3D7, probes)

chromosome_map(
  genome_Pf3D7,
  probes,
  "karyoploteR",
  title = "Example Chromosome Map",
  colours = c("#006A8EFF", "#A8A6A7FF", "#B1283AFF")
)
# ->
plot_karyoploteR(
  genome_Pf3D7,
  probes,
  title = "Example Chromosome Map",
  colours = c("#006A8EFF", "#A8A6A7FF", "#B1283AFF")
)

bailey-lab/miplicorn documentation built on March 19, 2023, 7:40 p.m.