5 CNEs visualisation
To visualise the CNEs together with other gene annotations, we choose to use the Bioconductor package Gviz in this vignette. Gviz, based on the grid graphics scheme, is a very powerful package for plotting data and annotation information along genomic coordinates. The functionality of integrating publicly available genome annotation data, such as UCSC or Ensembl, significantly reduced the burden of preparing annotations for common assemblies. Since the Bioconductor release 2.13 of Gviz, it provides the data track in horizon plot, which exactly meets our needs for visualisation of CNEs density plots. For more detailed usage, please check the vignette or manual of Gviz.
Another option for visualisation is the package ggbio, which is based on ggplot2. The advantage of ggbio is the simplicity of adding any customised ggplot2 style track into the plot without tuning the coordinate systems. The densities generated in the following section can be easily plot in the horizon plot. A short straightforward tutorial regarding horizon plot in ggplot2 format is available from http://timelyportfolio.blogspot.co.uk/2012/08/horizon-on-ggplot2.html.
5.1 Gene annotation visualisation
For the example of hg19 vs danRer7 in this vignette, we choose hg19 as the reference and show the range of developmental gene PAX6.
library(Gviz)
genome <- "hg19"
chr <- "chr11"
start <- 31000000L
end <- 33000000L
axisTrack <- GenomeAxisTrack()
ideoTrack <- IdeogramTrack(genome=genome, chromosome=chr)
cpgIslands <- UcscTrack(genome=genome, chromosome=chr,
track="cpgIslandExt", from=start, to=end,
trackType="AnnotationTrack", start="chromStart",
end="chromEnd", id="name", shape="box",
fill="#006400", name="CpG Islands")
refGenes <- UcscTrack(genome="hg19", chromosome=chr,
track="refGene", from=start, to=end,
trackType="GeneRegionTrack", rstarts="exonStarts",
rends="exonEnds", gene="name2", symbol="name2",
transcript="name", strand="strand", fill="#8282d2",
name="refSeq Genes", collapseTranscripts=TRUE)
biomTrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr,
start=start , end=end, name="Ensembl")library(Gviz)
plotTracks(list(axisTrack, ideoTrack, cpgIslands, refGenes),
collapseTranscripts=TRUE, shape="arrow",
showId=TRUE, transcriptAnnotation="symbol")
It is also possible to plot the annotation from an ordinary R object, such as data.frame, GRanges, IRanges or even from a local file. Usually the gff file containing the gene annotation can be processed by Gviz directly. For more details, please look into the vignette of Gviz.
5.2 CNEs horizon plot
dbName <- file.path(system.file("extdata", package="CNEr"),
"cne.sqlite")
windowSize <- 300L
minLength <- 50L
cneHg19DanRer7_45_50 <-
CNEDensity(dbName=dbName,
tableName="danRer7_hg19_45_50",
assembly1="hg19", chr=chr, start=start,
end=end, windowSize=windowSize,
minLength=minLength)
cneHg19DanRer7_48_50 <-
CNEDensity(dbName=dbName,
tableName="danRer7_hg19_48_50",
assembly1="hg19", chr=chr, start=start,
end=end, windowSize=windowSize,
minLength=minLength)
cneHg19DanRer7_49_50 <-
CNEDensity(dbName=dbName,
tableName="danRer7_hg19_49_50",
assembly1="hg19", chr=chr, start=start,
end=end, windowSize=windowSize,
minLength=minLength)data(cneHg19DanRer7_45_50)
data(cneHg19DanRer7_48_50)
data(cneHg19DanRer7_49_50)
genome <- "hg19"
chr <- "chr11"
start <- 31000000L
end <- 33000000L
#axisTrack = GenomeAxisTrack()
#ideoTrack = IdeogramTrack(genome=genome, chromosome=chr)
strand <- "+"
dataMatrix <- cneHg19DanRer7_45_50
dTrack1 <- DataTrack(start=dataMatrix[ ,1], end=dataMatrix[ ,1],
data=dataMatrix[ ,2], chromosome=chr, strand=strand,
genome=genome, type="horiz", horizon.scale=0.1,
fill.horizon=c("#B41414", "#E03231", "#F7A99C",
"yellow", "orange", "red"),
name="danRer7 45/50")
dataMatrix <- cneHg19DanRer7_48_50
dTrack2 <- DataTrack(start=dataMatrix[ ,1], end=dataMatrix[ ,1],
data=dataMatrix[ ,2], chromosome=chr, strand=strand,
genome=genome, type="horiz", horizon.scale=0.1,
fill.horizon=c("#B41414", "#E03231", "#F7A99C",
"yellow", "orange", "red"),
name="danRer7 48/50")
dataMatrix <- cneHg19DanRer7_49_50
dTrack3 <- DataTrack(start=dataMatrix[ ,1], end=dataMatrix[ ,1],
data=dataMatrix[ ,2], chromosome=chr, strand=strand,
genome=genome, type="horiz", horizon.scale=0.1,
fill.horizon=c("#B41414", "#E03231", "#F7A99C",
"yellow", "orange", "red"),
name="danRer7 49/50")plotTracks(list(axisTrack, ideoTrack, cpgIslands,
refGenes,
dTrack1, dTrack2, dTrack3),
collapseTranscripts=TRUE, shape="arrow",
showId=TRUE, transcriptAnnotation="symbol")
From this horizon plot compared with Zebrafish with Human as reference genome, the developmental gene PAX6 was surrounded by the density peaks of CNEs.