Entering edit mode
Janet Young
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740
@janet-young-2360
Last seen 5.1 years ago
Fred Hutchinson Cancer Research Center,…
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
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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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