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first of all thank you for your great work... however, lately after upgrading R to version 3, ggbio::autoplot() stopped working for me when using on TranscriptDb objects:
autoplot(txdb, GRanges("chr9…
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Hi Tengfei,
I think the methods to handle GappedAlignments in bioconductor 2.12 need to be changed in work with GAlignments.
regards,
Jonas
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform…
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I figured out the following snippet to draw the read coverage plot:
```
autoplot( xinli.test.gene, geom = 'polygon', stat = 'coverage',
coverage.col = 'green', fill = 'green', alpha…
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Right now, 'y' is a required parameter for stat="aggregate". Why not generate an automatic 'y' using the coverage? This would then be a smoothing of the coverage. Another idea would be to use the 'sco…
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When using `ggbio::autoplot` and `geom_alignment` on `CompressedGRangesList` and `GRanges`, ggplot throw warnings for unknown parameters. (`group.selfish ` for `CompressedGRangesList`, `label, utr.ge…
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Plotting a few sample coordinates, appears they are plotting out of range of the chromosomal boundaries. I double checked to ensure none of these coordinates are outside of the boundary
> myGranges…
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```
library(IRanges)
.zoom0 length(x) && length(z) != 1L)
stop("'z' is longer than 'x'")
if (anyNA(z) || min(z)
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Since we want to reach as many people as possible we should provide the conda recipe for easy setup of environment, but pointing out the benefits of guix in a hpc environment and maybe link to guix-hp…
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Hi,
I just started using ggbio in order to plot gene tracks along with ggplots.
When i try to add variant information as a new track i have problems creating the track:
Code used:
```R
vc…
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This code: "autoplot(gra, aes(fill = group, group = group), geom = "alignment")" results in each group being given a separate 'y' coordinate. Why then do we not just use 'y' as the aesthetic? If we co…