[BioC] change Gviz point size?

[James W. MacDonald]

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 at 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