Question: Gviz : fill and line arrow color issues
gravatar for Nicolas Rosewick
4.0 years ago by
Belgium, Brussels
Nicolas Rosewick8.7k wrote:


I've an issue to plot a figure using Gviz? I've a dataframe containing several genomic positions (chr, pos, strand) and want to plot a specific region containing these features. The strand information is important in this plot thus I would like to use the arrow shape and a specific color to highlight it (strand + = red ; "-" = blue). I want only the arrow border line to be colored, and white within it. Thus I will us the "col" parameter (and will put the fill parameter to "white")

So :

# specify color for each features
col <- df$strand
# create track containing the colored line
aTrack <- AnnotationTrack(start=df$pos,width=1000,chromosome="chr15",strand=t$strand,genome="hg19",col=col,name="foo",fill="white")
# create track where the whole arrow is colored
bTrack <- AnnotationTrack(start=df$pos,width=1000,chromosome="chr15",strand=t$strand,genome="hg19",fill=col,name="foo")
# plot both tracks

Here's the results : enter image description here

You can see that the second track colored the arrows in the right manner (majority of blue ones and a few red ones), but for the first track all the arrow are red ... even though I use the same variable to assign the colors.

Anyone can help me?

Here's my session info :

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=fr_BE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_BE.UTF-8        LC_COLLATE=fr_BE.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.7      
[4] BiocGenerics_0.8.0   Gviz_1.6.0           ggplot2_1.0.1       

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3        AnnotationDbi_1.24.0   Biobase_2.22.0        
 [4] biomaRt_2.18.0         Biostrings_2.30.1      biovizBase_1.10.8     
 [7] bitops_1.0-6           BSgenome_1.30.0        cluster_2.0.3         
[10] colorspace_1.2-6       DBI_0.3.1              dichromat_2.0-0       
[13] digest_0.6.9           foreign_0.8-66         Formula_1.2-1         
[16] GenomicFeatures_1.14.5 gridExtra_2.2.1        gtable_0.2.0          
[19] Hmisc_3.17-0           labeling_0.3           lattice_0.20-33       
[22] latticeExtra_0.6-28    magrittr_1.5           MASS_7.3-31           
[25] munsell_0.4.3          nnet_7.3-12            plyr_1.8              
[28] proto_0.3-10           RColorBrewer_1.1-2     RCurl_1.95-4.1        
[31] reshape2_1.2.2         rpart_4.1-10           Rsamtools_1.14.3      
[34] RSQLite_0.11.4         rtracklayer_1.22.7     scales_0.2.4          
[37] splines_3.0.1          stats4_3.0.1           stringi_1.0-1         
[40] stringr_1.0.0          survival_2.38-3        tools_3.0.1           
[43] XML_3.98-1.1           zlibbioc_1.8.0


gviz • 2.1k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Nicolas Rosewick8.7k
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