layout_karyogram-method: Create a karyogram layout

In tengfei/ggbio: Visualization tools for genomic data

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(GenomeInfoDb)
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()

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.