[BioC] ggbio tracks with labelled: problem when I add a main title

Janet Young jayoung at fhcrc.org
Thu Dec 5 00:32:04 CET 2013

Hi there,

I think I found a problem with the way ggbio handles track labels when I add a main title to the plot.  I think the code I've included below should demonstrate the problem, but let me know if it's not clear. 

(and thanks for the nice package!)



## example tracks (taken from ?tracks)
df1 <- data.frame(time = 1:100, score = sin((1:100)/20)*10)
p1 <- qplot(data = df1, x = time, y = score, geom = "line")
df2 <- data.frame(time = 30:120, score = sin((30:120)/20)*10, value = rnorm(120-30 + 1))
p2 <- ggplot(data = df2, aes(x = time, y = score)) + 
  geom_line() + geom_point(size = 4, aes(color = value))

### plot two tracks with a label - this looks OK
tracks (p1, p2, main="myTitle")

### plot two labelled tracks - this look OK
tracks (p1=p1, p2=p2)

### adding title to the plot with labelled tracks messes up alignment of the labels with the plot
tracks (p1=p1, p2=p2, main="myTitle")


R Under development (unstable) (2013-11-06 r64163)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] ggbio_1.11.7    ggplot2_0.9.3.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.25.9     Biobase_2.23.3           BiocGenerics_0.9.1      
 [4] biomaRt_2.19.1           Biostrings_2.31.3        biovizBase_1.11.6       
 [7] bitops_1.0-6             BSgenome_1.31.7          cluster_1.14.4          
[10] colorspace_1.2-4         DBI_0.2-7                dichromat_2.0-0         
[13] digest_0.6.4             Formula_1.1-1            GenomicAlignments_0.99.4
[16] GenomicFeatures_1.15.4   GenomicRanges_1.15.10    grid_3.1.0              
[19] gridExtra_0.9.1          gtable_0.1.2             Hmisc_3.13-0            
[22] IRanges_1.21.13          labeling_0.2             lattice_0.20-24         
[25] MASS_7.3-29              munsell_0.4.2            parallel_3.1.0          
[28] plyr_1.8                 proto_0.3-10             RColorBrewer_1.0-5      
[31] RCurl_1.95-4.1           reshape2_1.2.2           Rsamtools_1.15.12       
[34] RSQLite_0.11.4           rtracklayer_1.23.3       scales_0.2.3            
[37] splines_3.1.0            stats4_3.1.0             stringr_0.6.2           
[40] survival_2.37-4          tools_3.1.0              VariantAnnotation_1.9.13
[43] XML_3.98-1.1             XVector_0.3.2            zlibbioc_1.9.0          


Dr. Janet Young 

Malik lab

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., A2-025, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 4512
email: jayoung  ...at...  fhcrc.org


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