plotStackedOverview: Plot stacked overview

In tengfei/ggbio: Visualization tools for genomic data

Plot stacked overview

Description

Plot stacked overview for genome with or without cytobands. It's a wrapper around layout_karyogram.

Usage

plotStackedOverview(obj, ..., xlab, ylab, main, geom = "rect",
                         cytobands = FALSE, rescale = TRUE,
                         rescale.range = c(0, 10))
plotKaryogram(obj, ..., xlab, ylab, main, geom = "rect",
                         cytobands = FALSE, rescale = TRUE,
                         rescale.range = c(0, 10))

Arguments

obj	a GRanges object, which could contain extra information about cytobands. If it's missing, will ask user to provide species information and download proper data set from UCSC. 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.
...	arguments passed to graphic functions to control aesthetics. For example, if you use geom "point", you need to provide "y" in aes(), and if can also pass color, fill, size etc. to control graphics.
xlab	label for x
ylab	label for y
main	title for plot.
geom	geom plotted on the stacked layout. Default is "rect", which showing interval data as rectangles. It automatically figures out boundary so you don't have to provide information in aes, users could specify other supported geom works for data.frame.
cytobands	logical value. Default is FALSE. If TRUE, plotting cytobands, this require your data have arbitrary column as name and gieStain. the easiest way is to use getIdeogram to get your data. Notice for this function, when cytobands is TRUE, it will only plot cytobands without overlaying your data. If you really need to overlay extra data on cytobands, please plus layout_karyogram for that purpose.
rescale	logical value. Default is TRUE, which rescale your data into the rescale.range, this make sure your data will not be plotted outside the stacked overview box.
rescale.range	Numeric range of length 2. Default is (0, 10), because stacked layout draws a white background as chromosome space and this space is of height 10. We hide the y-axis since we don't need it for stacked overview. Sometime users may want to leave some margin for their data, they can use this arguments to control the rescale.

Details

Stacked overview is just a arbitrary layout for karyogram layout, it use facets seqnaems ~ . as default to stack the genome. For accurate mapping, you need to provide seqlengths information in your GRanges object. Otherwise, data space will be computed for stacked overview chromosome background, this is _NOT_ the actual chromosome space!.

Value

A ggplot object.

Author(s)

Tengfei Yin

Examples

## Not run: 
library(biovizBase)
data(hg19IdeogramCyto, package = "biovizBase")
library(GenomicRanges)

## you can also get ideogram by biovizBase::getIdeogram

## make shorter and clean labels
old.chrs <- seqnames(seqinfo(hg19IdeogramCyto))
new.chrs <- gsub("chr", "", old.chrs)
## lst <- as.list(new.chrs)
names(new.chrs) <- old.chrs
new.ideo <- renameSeqlevels(hg19IdeogramCyto, new.chrs)
new.ideo <- keepSeqlevels(new.ideo, c(as.character(1:22) , "X", "Y"))
new.ideo


## sample data
data(darned_hg19_subset500, package = "biovizBase")
idx <- is.na(values(darned_hg19_subset500)$exReg)
values(darned_hg19_subset500)$exReg[idx] <- "unknown"

## you need to add seqlengths for accruate mapping
chrnames <- unique(as.character(seqnames(darned_hg19_subset500)))
data(hg19Ideogram, package = "biovizBase")
seqlengths(darned_hg19_subset500) <- seqlengths(hg19Ideogram)[sort(chrnames)]


dn <- darned_hg19_subset500
values(dn)$score <- rnorm(length(dn))

## plotStackedOverview is a simple wrapper around this functions to
   create a stacked layout
plotStackedOverview(new.ideo, cytobands = TRUE)

plotStackedOverview(dn)
plotStackedOverview(dn, aes(color = exReg, fill = exReg))
## this will did the trick for you to rescale the space
plotStackedOverview(dn, aes(x = midpoint, y = score), geom = "line")
plotStackedOverview(dn, aes(x = midpoint, y = score), geom = "line", rescale.range = c(4, 6))
## no rescale
plotStackedOverview(dn, aes(x = midpoint, y = score), geom = "line", rescale = FALSE,
                    xlab = "xlab", ylab = "ylab", main  = "main") + ylab("ylab")

## no object? will ask you for species and query the data on the fly
plotStackedOverview()
plotStackedOverview(cytobands = TRUE)

## End(Not run)

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