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

[jayoung]

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, or not reproducible for you.

(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

---

[lcolladotor]

I have seen the same issue, illustrated with a different example at https://stat.ethz.ch/pipermail/bioconductor/2013-December/056502.html

[lcolladotor]

Note that you can use version 1.8.8 which doesn't have this issue http://master.bioconductor.org/packages/2.12/bioc/html/ggbio.html

[ringprince]

Has there been progress on this one? Is it fixed in SVN (I have not tried the SVN version)?

[lcolladotor]

Hi,

I haven't heard of any progress on this issue. I just double checked, and the issue is still present in Bioc-release ggbio 1.10.10 and Bioc-devel 1.11.9

Best, Leo

[ringprince]

Hi Leo,

thanks for the info! Too bad this is not addressed yet. So, I am stuck at 1.8...

[tengfei]

Hi guys, so sorry for the super late reply, I just confirmed the bug and will work on fixing that this week!

On Thu, Jan 23, 2014 at 4:20 PM, ringprince [email protected]:

Hi Leo,

thanks for the info! Too bad this is not addressed yet. So, I am stuck at 1.8...

Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/48#issuecomment-33169782 .

[lcolladotor]

Thanks for the good news tengfei!

[tengfei]

This is just fixed in ggbio 1.11.10 in devel.

On Mon, Feb 3, 2014 at 11:36 AM, Leonardo Collado-Torres < [email protected]> wrote:

Thanks for the good news tengfei!

Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/48#issuecomment-33972424 .

[jayoung]

looks good - thanks very much, Tengfei,

Janet

On Feb 3, 2014, at 5:26 PM, Tengfei Yin wrote:

This is just fixed in ggbio 1.11.10 in devel.

On Mon, Feb 3, 2014 at 11:36 AM, Leonardo Collado-Torres < [email protected]> wrote:

Thanks for the good news tengfei!

Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/48#issuecomment-33972424 .

— Reply to this email directly or view it on GitHub.

[lcolladotor]

We should close this issue now that it has been solved