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Create annotated chromosome map

Source: R/chromosome-map.R
chromosome-map.Rd

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

Usage

plot_chromoMap(genome, probes, title = "", colours = list(), ...)

plot_karyoploteR(genome, probes, 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.

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.

See also

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

Examples

if (FALSE) { # interactive()
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"
)
single_probe <- tibble::tribble(
  ~chrom, ~start, ~end, ~probe_set,
  "chr14", 2342135L, 2342284L, "IBC",
  "chr5", 482233L, 482391L, "IBC",
  "chr9", 375274L, 375417L, "IBC",
  "chr14", 1401991L, 1402160L, "IBC",
  "chr10", 93054L, 93223L, "IBC",
  "chr7", 162127L, 162277L, "IBC"
)

plot_chromoMap(genome_Pf3D7, probes)
plot_chromoMap(genome_Pf3D7, single_probe, colours = "red")

plot_karyoploteR(genome_Pf3D7, single_probe)
plot_karyoploteR(
  genome_Pf3D7,
  probes,
  title = "Example Chromosome Map",
  colours = c("#006A8EFF", "#A8A6A7FF", "#B1283AFF")
)
}