Initialize the circular layout with an ideogram

circos.initializeWithIdeogram(
    cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"),
    species = NULL,
    sort.chr = TRUE,
    chromosome.index = usable_chromosomes(species),
    major.by = NULL,
    plotType = c("ideogram", "axis", "labels"),
    track.height = NULL,
    ideogram.height = convert_height(2, "mm"),
    ...)

Arguments

cytoband	A path of the cytoband file or a data frame that already contains cytoband data. By default it is cytoband for hg19. Pass to `read.cytoband`.
species	Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download cytoBand.txt.gz from UCSC website automatically. If there is no cytoband for user's species, it will keep on trying to download chromInfo file. Pass to `read.cytoband` or `read.chromInfo`.
chromosome.index	subset of chromosomes, also used to reorder chromosomes.
sort.chr	Whether chromosome names should be sorted (first sort by numbers then by letters). If `chromosome.index` is set, this argumetn is enforced to `FALSE`
major.by	Increment of major ticks. Pass to `circos.genomicInitialize`.
plotType	Which tracks should be drawn. `ideogram` for ideogram rectangle, `axis` for genomic axis and `labels` for chromosome names. If there is no ideogram for specified species, `ideogram` will be enforced to be excluded. If it is set to `NULL`, the function just initialize the plot but draw nothing.
track.height	Height of the track which contains "axis" and "labels".
ideogram.height	Height of the ideogram track
...	Pass to `circos.genomicInitialize`.

Details

The function will initialize the circular plot in which each sector corresponds to a chromosome. You can control the order of chromosomes by chromosome.index or by sort.chr, or by setting a special format of cytoband (please refer to read.cytoband to find out how to control a proper cytoband).

The function finally pass data to circos.genomicInitialize to initialize the circular plot.

The style of ideogram is almost fixed, but you can customize it with your self-sefined code. Refer to vignette for demonstration.

Examples

# \donttest{
circos.initializeWithIdeogram()

cytoband.file = system.file(package = "circlize",
    "extdata", "cytoBand.txt")
circos.initializeWithIdeogram(cytoband.file)

cytoband.df = read.table(cytoband.file, colClasses = c("character", "numeric",
    "numeric", "character", "character"), sep = "\t")
circos.initializeWithIdeogram(cytoband.df)

circos.initializeWithIdeogram(species = "hg18")

circos.initializeWithIdeogram(species = "mm10")

circos.initializeWithIdeogram(chromosome.index = c("chr1", "chr2"))

cytoband = read.table(cytoband.file, colClasses = c("character", "numeric",
    "numeric", "character", "character"), sep = "\t")
circos.initializeWithIdeogram(cytoband, sort.chr = FALSE)

cytoband[[1]] = factor(cytoband[[1]], levels = paste0("chr", c(22:1, "X", "Y")))
circos.initializeWithIdeogram(cytoband, sort.chr = FALSE)

cytoband = read.table(cytoband.file, colClasses = c("character", "numeric",
    "numeric", "character", "character"), sep = "\t")
circos.initializeWithIdeogram(cytoband, sort.chr = TRUE)

circos.initializeWithIdeogram(plotType = c("axis", "labels"))

circos.initializeWithIdeogram(plotType = NULL)

circos.par("start.degree" = 90)
#> Warning: 'start.degree' can only be modified before `circos.initialize`, or
#> maybe you forgot to call `circos.clear` in your last plot.
circos.initializeWithIdeogram()
circos.clear()

circos.par("gap.degree" = rep(c(2, 4), 12))
circos.initializeWithIdeogram()
circos.clear()
# }

Initialize the circular layout with an ideogram

Arguments

Details

See also

Examples