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Question: Gviz AnnotationTrack id above feature
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gravatar for bruce.moran
18 months ago by
bruce.moran20
Ireland
bruce.moran20 wrote:

Hi,

hoping one of the Gviz team can help me with this (mostly so I can thank you for the really flexible package!).

Example data:

cpgGR <- makeGRangesFromDataFrame(data.frame(chrom = c(1,1), start = c(23884842, 23885682), end = c(23885087, 23886212)))
ids <- c("CpG:23", "CpG:49")
cpgTrack <- AnnotationTrack(cpgGR, id = ids, name = "CpG Islands",  showID = TRUE, genome = "hg19", cex = .6, fill = "lightgreen", fontcolor = "black", just.group = "above")

plotTracks(list(cpgTrack),  legend = TRUE, showFeatureId = TRUE, just.group = "above")

 

But this does not either make the text black, nor place the IDs above the feature. I believe this to be possible, can someone specify how?

 

Many thanks,

 

Bruce.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] coMET_1.6.0          trackViewer_1.10.2   psych_1.7.3.21
 [4] biomaRt_2.30.0       biovizBase_1.22.0    ggbio_1.22.3
 [7] ggplot2_2.2.1        AnnotationHub_2.6.4  Gviz_1.18.1
[10] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2  IRanges_2.8.1
[13] S4Vectors_0.12.1     BiocGenerics_0.20.0

 

ADD COMMENTlink modified 18 months ago by florian.hahne@novartis.com1.6k • written 18 months ago by bruce.moran20
2
gravatar for florian.hahne@novartis.com
18 months ago by
Switzerland

How about this:

plotTracks(list(cpgTrack),  legend = TRUE, groupAnnotation="id", just.group = "above")
ADD COMMENTlink written 18 months ago by florian.hahne@novartis.com1.6k

Thanks Florian, much appreciated!

Bruce.

ADD REPLYlink written 18 months ago by bruce.moran20
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