Hi Jim, I made a silly mistake on "cex", I was modifying one functions but ran another one All my fault. "cex" is the right parameter. Sincerely, Chunxuan > Date: Tue, 19 Nov 2013 09:46:00 -0500 > From: jmacdon@uw.edu > To: chunxuan@outlook.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] change Gviz point size? > > Hi Chunxuan, > > On Tuesday, November 19, 2013 8:41:57 AM, shao chunxuan wrote: > > > > > > > > Hi, > > How to change the point size in the DataTrack? I changed the "cex" parameter in "DataTrack" but it seems no effect.My code is: > > dtrack <- DataTrack(..., baseline = 0, col = "grey", col.line = "red", pch = 20, cex = 5) > > Any suggestions to make the point smaller? > > You certainly won't make the points smaller by using a cex value of 5 > (which means 'make the points 5 times larger than usual'). > > Plus, without giving a reproducible example, how is anybody supposed to > help you? For instance, the code you give above won't work, so you are > just giving some random, non-functional code. That is less than > helpful. So here is an example of something that people could have used > to see what you mean: > > library(Gviz) > data(twoGroups) > trk <- DataTrack(twoGroups, cex = 5, baseline=0, col="grey", > col.line="red", pch=20) > plotTracks(trk) > > This shows that the cex argument does exactly what it is supposed to > do, and the plotting symbols are gigantic. So let's try a reasonable > cex argument: > > trk <- DataTrack(twoGroups, cex = 0.5, baseline=0, col="grey", > col.line="red", pch=20) > plotTracks(trk) > > And that works just as advertized. > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Gviz_1.6.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.25.2 Biobase_2.22.0 BiocGenerics_0.8.0 > [4] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.3 > [7] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 > [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 > [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 Hmisc_3.12-2 > [16] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 > [19] latticeExtra_0.6-26 munsell_0.4.2 parallel_3.0.2 > [22] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [25] rpart_4.1-3 Rsamtools_1.14.1 RSQLite_0.11.4 > [28] rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 > [31] stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 > [34] XVector_0.2.0 zlibbioc_1.8.0 > > > > Best, > > Jim > > > > > >> sessionInfo()R version 3.0.2 (2013-09-25)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] parallel graphics grDevices utils datasets stats grid [8] methods base > > other attached packages: [1] Gviz_1.6.0 RColorBrewer_1.0-5 biomaRt_2.18.0 [4] org.Hs.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [7] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 [10] pheatmap_0.7.7 ggplot2_0.9.3.1 reshape2_1.2.2 [13] plyr_1.8 > > loaded via a namespace (and not attached): [1] Biostrings_2.30.0 biovizBase_1.10.3 bitops_1.0-6 [4] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 [7] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.14.0[10] GenomicRanges_1.14.1 gtable_0.1.2 Hmisc_3.12-2 [13] IRanges_1.20.0 labeling_0.2 lattice_0.20-24 [16] latticeExtra_0.6-26 MASS_7.3-29 munsell_0.4.2 [19] proto_0.3-10 RCurl_1.95-4.1 rpart_4.1-3 [22] Rsamtools_1.14.1 rtracklayer_1.22.0 scales_0.2.3 [25] stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [28] XML_3.95-0.2 XVector_0.2.0 zlibbioc_1.8.0 > > Best, Chunxuan > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 [[alternative HTML version deleted]]