Hi Janet,

I confirmed this, thanks for reporting, I will fix the bug today!

cheers

Tengfei


On Wed, Dec 4, 2013 at 6:50 PM, Janet Young <jayoung@fhcrc.org> wrote:

> (I also just found the ggbio github bug tracker - submitted this over
> there, too - sorry about the double-post)
>
>
> On Dec 4, 2013, at 3:32 PM, Janet Young wrote:
>
> > 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!)
> >
> > Janet
> >
> >
> > library(ggbio)
> >
> > ## 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")
> >
> > sessionInfo()
> >
> > R Under development (unstable) (2013-11-06 r64163)
> > 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] 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
> > http://research.fhcrc.org/malik/en.html
> >
> > 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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>



-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

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