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\name{circos.initializeWithIdeogram}
\alias{circos.initializeWithIdeogram}
\title{
Initialize the circular layout with an ideogram
}
\description{
Initialize the circular layout with an ideogram
}
\usage{
circos.initializeWithIdeogram(cytoband = system.file(package = "circlize",
"extdata", "cytoBand.txt"), species = NULL, sort.chr = TRUE,
chromosome.index = NULL, major.by = NULL,
plotType = c("ideogram", "axis", "labels"),
track.height = NULL, ideogram.height = convert_height(2, "mm"),
...)
}
\arguments{
\item{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 \code{\link{read.cytoband}}.
}
\item{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 \code{\link{read.cytoband}} or \code{\link{read.chromInfo}}.
}
\item{chromosome.index}{subset of chromosomes, also used to reorder chromosomes.
}
\item{sort.chr}{Whether chromosome names should be sorted (first sort by numbers then by letters).
If \code{chromosome.index} is set, this argumetn is enforced to \code{FALSE}
}
\item{major.by}{Increment of major ticks. Pass to \code{\link{circos.genomicInitialize}}.
}
\item{plotType}{Which tracks should be drawn. \code{ideogram} for ideogram rectangle, \code{axis} for genomic axis and \code{labels} for chromosome names.
If there is no ideogram for specified species, \code{ideogram} will be enforced to be excluded.
If it is set to \code{NULL}, the function just initialize the plot but draw nothing.
}
\item{track.height}{Height of the track which contains "axis" and "labels".
}
\item{ideogram.height}{Height of the ideogram track
}
\item{...}{Pass to \code{\link{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 \code{chromosome.index} or by \code{sort.chr}, or by setting a special format of \code{cytoband} (please refer to \code{\link{read.cytoband}}
to find out how to control a proper \code{cytoband}).
The function finally pass data to \code{\link{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.
}
\references{
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
}
\examples{
\dontrun{
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)
circos.initializeWithIdeogram()
circos.clear()
circos.par("gap.degree" = rep(c(2, 4), 12))
circos.initializeWithIdeogram()
circos.clear()
}
}
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