Setup ideograms

Source: R/utils_ideograms.R

Sets up a local cache of ideogram data for a genome.

setup_ideograms(
  data = NULL,
  genome = NULL,
  colourmap = default_ideogram_colours()
)

Arguments

data

One of the following:

  • A data.frame with the following 6 columns:

    chrom

    A character column with chromosome names.

    chromStart

    An integer vector with band start positions.

    chromEnd

    An integer vector with band end positions.

    name

    A character with names for cytogenetic bands.

    gieStain

    A character with Giemsa stain results. Recognised values are: "gneg", "gpos", "gpos50", "gpos75", "gpos25", "gpos100", "acen", "gvar", and "stalk".

  • A character with the filename from which the data are to be read from.

  • Can be missing if the genome argument is set. See details.
genome

A character with the genome name, e.g. "mm10".
colourmap

A named character vector with colours where names correspond to the gieStain column.

Value

Returns no value, but caches the ideograms under the genome identifier in a temporary cache.

Details

If the data argument is missing but the genome argument is either "hg19", "hg38", "mm9" or "mm10", BiocFileCache is used to cache the cytoBand.txt file from UCSC.

Methods (by class)

  • data = data.frame,genome = ANY: Uses data.frame to generate ideograms

  • data = character,genome = ANY: Uses character as file path.

  • data = missing_OR_NULL,genome = character: Attempts to lookup genome in UCSC tables and caches this.

See also

This is to be used in conjunction with ideogram axes: guide_ideogram_axis()

Examples

setup_ideograms(genome = "hg38")
#> Ideograms already in cache. Overwiting previous cache.