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 [[alternative HTML version deleted]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Jianhong, the mountain type plot is supposed to emphasise differences in a profile relative to a baseline. Thus you need to define two colors for the fill. One is the color above that baseline and one the color below. Using your example this should illustrate what I mean: plotTracks(list(gcContent), from=from, to=to, showTitle=F, baseline=36) If you really want to force the plot type to give you a smoothed filled profile of your data you could do this: plotTracks(list(gcContent), from=from, to=to, showTitle=F, fill.mountain=rep("black",2)) By default the mountain plot computes a loess smoothing for your data, but I see that you are already creating the object using a running window smoother. Not sure whether this is intentional or not, but you may want to consider just using one of the two smoothing options. If all you want is a filled profile, the 'histogram' type may be a lot more flexible: plotTracks(list(gcContent), from=from, to=to, showTitle=F, type="histogram") Hope that helps, Florian From: <ou>, Jianhong <jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>> Date: Monday, September 9, 2013 6:30 PM To: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Cc: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: howto plot a figure like UCSC genome browser by Gviz 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 [[alternative HTML version deleted]]