layout_karyogram {ggbio} | R Documentation

## Create a karyogram layout

### Description

Create a karyogram layout.

### Usage

    ## S4 method for signature 'GRanges'
    layout_karyogram(data, ..., xlab, ylab, main,
              facets = seqnames ~ ., cytobands = FALSE, geom = "rect",
              stat = NULL, ylim = NULL, rect.height = 10)

### Arguments

`data` | a `GRanges` object, which could contain extra information about cytobands. If you want an accurate genome mapping, please provide `seqlengths` with this `GRanges` object,otherwise it will emit a warning and use data space to estimate the chromosome space which is very rough.
`...` | Extra parameters such as aes() or arbitrary `color` and `size`.
`xlab` | character vector or expression for x axis label.
`ylab` | character vector or expression for y axis label.
`main` | character vector or expression for plot title.
`facets` | faceting formula to use.
`cytobands` | logical value indicate to show the cytobands or not.
`geom` | The geometric object to use display the data.
`stat` | character vector specifying statistics to use.
`ylim` | limits for y axis, usually the chromosome spaces y limits are from 0 to rect.height, which 10, so if you wan to stack some data on top of it, you can set limits to like c(10, 20).
`rect.height` | numreic value indicate half of the rectangle ploting region, used for alignment of multiple layers.

### Value

A 'Layer'.

### Author(s)

Tengfei Yin

### Examples

    ### R code from vignette source 'karyogram.Rnw'

    ###################################################
    ### code chunk number 1: loading
    ###################################################
    library(ggbio)
    data(hg19IdeogramCyto, package = "biovizBase")
    head(hg19IdeogramCyto)
    ## default pre-set color stored in
    getOption("biovizBase")$cytobandColor

    ###################################################
    ### code chunk number 2: default
    ###################################################
    autoplot(hg19IdeogramCyto, layout = "karyogram", cytobands = TRUE)

    ###################################################
    ### code chunk number 3: change-order
    ###################################################
    library(GenomicRanges)
    hg19 <- keepSeqlevels(hg19IdeogramCyto, paste0("chr", c(1:22, "X", "Y")))
    head(hg19)
    autoplot(hg19, layout = "karyogram", cytobands = TRUE)

    ###################################################
    ### code chunk number 4: cyto-normal
    ###################################################
    library(GenomicRanges)
    ## it's a 'ideogram'
    biovizBase::isIdeogram(hg19)
    ## set to FALSE
    autoplot(hg19, layout = "karyogram", cytobands = FALSE, aes(fill = gieStain)) +
      scale_fill_giemsa()

    ###################################################
    ### code chunk number 5: load-RNAediting
    ###################################################
    data(darned_hg19_subset500, package = "biovizBase")
    dn <- darned_hg19_subset500
    head(dn)
    ## add seqlengths
    ## we have seqlegnths information in another data set
    data(hg19Ideogram, package = "biovizBase")
    seqlengths(dn) <- seqlengths(hg19Ideogram)[names(seqlengths(dn))]
    ## now we have seqlengths
    head(dn)
    ## then we change order
    dn <- keepSeqlevels(dn, paste0("chr", c(1:22, "X")))
    autoplot(dn, layout = "karyogram")
    ## this equivalent to
    ## autoplot(seqinfo(dn))

    ###################################################
    ### code chunk number 6: load-RNAediting-color
    ###################################################
    ## since default is geom rectangle, even though it's looks like segment
    ## we still use both fill/color to map colors
    autoplot(dn, layout = "karyogram", aes(color = exReg, fill = exReg))

    ###################################################
    ### code chunk number 7: load-RNAediting-color-NA
    ###################################################
    ## since default is geom rectangle, even though it's looks like segment
    ## we still use both fill/color to map colors
    autoplot(dn, layout = "karyogram", aes(color = exReg, fill = exReg)) +
      scale_color_discrete(na.value = "brown")

    ###################################################
    ### code chunk number 8: load-RNAediting-color-fake
    ###################################################
    dn2 <- dn
    seqlengths(dn2) <- rep(max(seqlengths(dn2)), length(seqlengths(dn2)) )
    autoplot(dn2, layout = "karyogram", aes(color = exReg, fill = exReg))

    ###################################################
    ### code chunk number 9: plotKaryogram (eval = FALSE)
    ###################################################
    ## plotKaryogram(dn)
    ## plotKaryogram(dn, aes(color = exReg, fill = exReg))

    ###################################################
    ### code chunk number 10: low-default
    ###################################################
    ## plot ideogram
    p <- ggplot(hg19) + layout_karyogram(cytobands = TRUE)
    p
    ## eqevelant autoplot(hg19, layout = "karyogram", cytobands = TRUE)

    ###################################################
    ### code chunk number 11: low-default-addon
    ###################################################
    p <- p + layout_karyogram(dn, geom = "rect", ylim = c(11, 21), color = "red")
    ## commented line below won't work
    ## the cytoband fill color has been used already.
    ## p <- p + layout_karyogram(dn, aes(fill = exReg, color = exReg), geom = "rect")
    p

    ###################################################
    ### code chunk number 12: edit-space
    ###################################################
    ## plot chromosome space
    p <- autoplot(seqinfo(dn))
    ## make sure you pass rect as geom
    ## otherwise you just get background
    p <- p + layout_karyogram(dn, aes(fill = exReg, color = exReg), geom = "rect")
    values(dn)$pvalue <- rnorm(length(dn))
    p + layout_karyogram(dn, aes(x = start, y = pvalue), ylim = c(10, 30), geom = "line", color = "red")
    p

    ###################################################
    ### code chunk number 13: sessionInfo
    ###################################################
    sessionInfo()

[Package ggbio version 1.32.0 Index]