Entering edit mode
Dear ggbio experts,
ggbio is an excellent package. Thanks for providing it. - One thing I
have not been able to figure out though is how to create mirrored
(~lacking better term here~) representations of coverage data. It is
not
hard to achieve this with ggplot2, but a ggbio solution would be much
more elegant and efficient. Here is an example illustrating what I
mean:
## Plotting coverage with ggbio using faceting for +/-
library(GenomicRanges); library(ggbio)
set.seed(1); N <- 100;
gr <- GRanges(seqnames = sample(c("chr1", "chr2", "chr3"), size = N,
replace = TRUE), IRanges(start = sample(1:300, size = N,
replace =
TRUE), width = sample(70:75, size = N,replace = TRUE)), strand
=
sample(c("+", "-"), size = N, replace = TRUE), value =
rnorm(N, 10, 3),
score = rnorm(N, 100, 30), sample = sample(c("Normal",
"Tumor"), size =
N, replace = TRUE), pair = sample(letters, size = N, replace =
TRUE))
autoplot(gr, aes(color = strand, fill = strand), facets = strand ~
seqnames, stat = "coverage")
## What if I want the following mirrored layout for +/- instead:
pos <- sapply(coverage(gr[strand(gr)=="+"]), as.numeric)
pos <- data.frame(Chr=rep(names(pos), sapply(pos, length)),
Strand=rep("+", length(unlist(pos))), Position=1:length(unlist(pos)),
Coverage=as.numeric(unlist(pos)))
neg <- sapply(coverage(gr[strand(gr)=="-"]), as.numeric)
neg <- data.frame(Chr=rep(names(neg), sapply(neg, length)),
Strand=rep("-", length(unlist(neg))), Position=1:length(unlist(neg)),
Coverage=-as.numeric(unlist(neg)))
covdf <- rbind(pos, neg)
p <- ggplot(covdf, aes(Position, Coverage, fill=Strand)) +
geom_bar(stat="identity", position="identity") +
facet_wrap(~Chr)
p
Is there a way achieving the latter with ggbio directly? Most
biologists would
prefer this mirrored over the faceted +/- representation. If this is
already
possible then perhaps this could be added to the ggbio documentation?
Thanks,
Thomas
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] ggbio_1.10.10 ggplot2_0.9.3.1 GenomicRanges_1.14.3
[4] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0
[4] Biostrings_2.30.1 biovizBase_1.10.5 bitops_1.0-6
[7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4
[10] DBI_0.2-7 dichromat_2.0-0 digest_0.6.3
[13] Formula_1.1-1 GenomicFeatures_1.14.2 grid_3.0.2
[16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.13-0
[19] labeling_0.2 lattice_0.20-24 MASS_7.3-29
[22] munsell_0.4.2 plyr_1.8 proto_0.3-10
[25] RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2
[28] Rsamtools_1.14.2 RSQLite_0.11.4
rtracklayer_1.22.0
[31] scales_0.2.3 splines_3.0.2 stats4_3.0.2
[34] stringr_0.6.2 survival_2.37-4 tools_3.0.2
[37] VariantAnnotation_1.8.7 XML_3.95-0.2 zlibbioc_1.8.0
