[BioC] howto plot a figure like UCSC genome browser by Gviz

[Robert Ivanek]

Dear Jianhong,

The parameter fill.mountain has to be a vector with 2 elements - colors.
First one is used for negative values and second one for positive ones.

Following piece of code should fill in the area in "black":


gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",
    track = "GC Percent", table = "gc5Base", from = from,
    to = to, trackType = "DataTrack", start = "start",
    end = "end", data = "score", type = "mountain", window = -1,
    windowSize = 1500, fill.mountain = c("black", "black"),
    col.mountain = "black", name = "GC Percent")


Best
Robert

On 09/09/13 18:30, Ou, Jianhong wrote:
> Dear all,
> 
> I want to plot a track via Gviz in mountain type. However, it looks like that fill.mountain does not work. How do I fill the area under the curve in black? Thanks.
> 
>> library(Gviz)
> Loading required package: grid
>> from <- 65921878
>> to <- 65980988
>> gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",
> +  track = "GC Percent", table = "gc5Base", from = from,
> +  to = to, trackType = "DataTrack", start = "start",
> +  end = "end", data = "score", type = "mountain", window = -1,
> +  windowSize = 1500, fill.mountain = "black",
> +  col.mountain = "black", name = "GC Percent")
>> plotTracks(list(gcContent), from=from, to=to, showTitle=F)
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] Gviz_1.4.5
> 
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.22.6   Biobase_2.20.1         BiocGenerics_0.6.0     biomaRt_2.16.0         Biostrings_2.28.0
>  [6] biovizBase_1.8.1       bitops_1.0-6           BSgenome_1.28.0        cluster_1.14.4         colorspace_1.2-2
> [11] DBI_0.2-7              dichromat_2.0-0        GenomicFeatures_1.12.3 GenomicRanges_1.12.5   Hmisc_3.12-2
> [16] IRanges_1.18.3         labeling_0.2           lattice_0.20-23        munsell_0.4.2          parallel_3.0.1
> [21] plyr_1.8               RColorBrewer_1.0-5     RCurl_1.95-4.1         rpart_4.1-3            Rsamtools_1.12.4
> [26] RSQLite_0.11.4         rtracklayer_1.20.4     scales_0.2.3           stats4_3.0.1           stringr_0.6.2
> [31] tools_3.0.1            XML_3.95-0.2           zlibbioc_1.6.0
> 
> 
> Yours sincerely,
> 
> Jianhong Ou
> 
> LRB 670A
> Program in Gene Function and Expression
> 364 Plantation Street Worcester,
> MA 01605
> 
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> 
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