layout_karyogram {ggbio} | R Documentation |
Create a karyogram layout.
## S4 method for signature 'GRanges' layout_karyogram(data, ..., xlab, ylab, main, facets = seqnames ~ ., cytoband = FALSE, geom = "rect", stat = NULL, ylim = NULL, rect.height = 10)
data |
a |
... |
Extra parameters such as aes() or arbitrary |
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. |
cytoband |
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. |
A 'Layer'.
Tengfei Yin
### 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", cytoband = 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", cytoband = TRUE) ################################################### ### code chunk number 4: cyto-normal ################################################### library(GenomicRanges) ## it's a 'ideogram' biovizBase::isIdeogram(hg19) ## set to FALSE autoplot(hg19, layout = "karyogram", cytoband = 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(cytoband = TRUE) p ## eqevelant autoplot(hg19, layout = "karyogram", cytoband = 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()