Create annotated chromosome map

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.

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"
)
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"
)

chromosome_map(genome_Pf3D7, single_probe, "karyoploteR")
#> Warning: `chromosome_map()` was deprecated in miplicorn 0.2.0.
#> The function has been deprecated in favor of `plot_chromoMap()` and
#>  `plot_karyoploteR()`.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
# ->
plot_karyoploteR(genome_Pf3D7, single_probe)


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

chromosome_map(genome_Pf3D7, single_probe, "chromoMap", colours = "red")
# ->
plot_chromoMap(genome_Pf3D7, single_probe, colours = "red")

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")
)