Description Usage Arguments Value Author(s) References Examples
View source: R/BiofeatureGraphics.R
Creates a ChromHMM track from a file of RoadMap using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.
1 2 3 | chromHMM_RoadMap(gen="hg19",chr, start, end, bedFilePath,
featureDisplay = 'all', colorcase='roadmap15',
title=" chromHMM RoadMap")
|
gen |
the name of the genome. Default value=hg19 |
chr |
The chromosome of interest |
start |
The starting position in the region of interest (the smallest value) |
end |
The end position in the region of interest (the largest value) |
bedFilePath |
The file path to the .BED file containing the data to be visualised |
featureDisplay |
A vector of features to be displayed, such as 1_TssA. Spelling and capitalisation of features must be identical to those in the user guide (in the 'State & Acronym' column). There are three possibilities. First, the visualisation of only one feature (e.g. featureDisplay <- "1_TssA"), only the name of the specific feature is required. Second, visualisation of a set of features, for this a vector of features is required (e.g. featureDisplay <- c("1_TssA","2_TssAFlnk")). Finally, visualison all features in the genomic region, achived by using the word "all" (e.g. featureDisplay <- "all"), "all" is set by default. You can find the complete list of features and their associated colours in the user guide. |
colorcase |
the type of colors used to visualise different elements contained in ROADmap data with 15-,18-,25- states. choice between roadmap15, roadmap18, comet18, roadmap25 and comet25. |
title |
The name of the annotation track |
An AnnotationTrack object of Gviz
Tiphaine Martin
Tom Hardiman
http://bioconductor.org/packages/release/bioc/html/Gviz.html
Got to RoadMap Epigenome
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | library("Gviz")
chr <- "chr1"
start <- 4500000
end <- 4600000
featureDisplay <- "7_Enh"
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")
if(interactive()){
chromHMM_RoadMapSingle <- chromHMM_RoadMap(gen="hg19",chr,start, end,
bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
plotTracks(chromHMM_RoadMapSingle, from = start, to = end)
} else {
data(chromHMM_RoadMapSingle)
plotTracks(chromHMM_RoadMapSingle, from = start, to = end)
}
######
library("Gviz")
chr <- "chr22"
start <- 38291000
end <- 38301200
featureDisplay <- c("7_Enh","13_ReprPC")
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")
if(interactive()){
chromHMM_RoadMapMultiple <- chromHMM_RoadMap(gen="hg19",chr,start, end,
bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
plotTracks(chromHMM_RoadMapMultiple, from = start, to = end)
} else {
data(chromHMM_RoadMapMultiple)
plotTracks(chromHMM_RoadMapMultiple, from = start, to = end)
}
#####
library("Gviz")
chr <- "chr22"
start <- 38291000
end <- 38301200
featureDisplay <- "all"
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")
if(interactive()){
chromHMM_RoadMapAll <- chromHMM_RoadMap(gen="hg19",chr,start, end,
bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
plotTracks(chromHMM_RoadMapAll, from = start, to = end)
} else {
data(chromHMM_RoadMapAll)
plotTracks(chromHMM_RoadMapAll, from = start, to = end)
}
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