User: bernatgel
bernatgel • 2.2k
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Posts by bernatgel
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6
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Answer:
A: Genome Browser Figure
... Since this question has been resurrected, I'll add [karyoploteR](https://bioconductor.org/packages/karyoploteR/) to the list of available tools. It's an R/Bioconductor package to plot data on genomes and can work with BAM files or BigWigs (and many other formats, actually).
At the [turorial page](h ...
written 3 hours ago by
bernatgel • 2.2k
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59
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... If you expect a deletion of 1 on the copies I'd go first with a copy-number calling (there are good tools working on WES) and then check if the variant frequencies (lack of heterozygous calls) support the call (you can use [CNVfilteR]( https://bioconductor.org/packages/CNVfilteR/) for that). I think ...
written 21 days ago by
bernatgel • 2.2k
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... If you have the length of your chromosomes or even an approximation, you should be able to plot them with [karyoploteR]( https://bioconductor.org/packages/karyoploteR/).
You'd need to build a custom genome (a GenomicRanges object with one range per chromosome) and you should be good to go. You can ...
written 28 days ago by
bernatgel • 2.2k
1
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1.2k
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Answer:
A: Plot SNPs on GViz
... You can do this with [karyoploteR](http://bioconductor.org/packages/karyoploteR) in combination with [ggplotify](https://cran.r-project.org/web/packages/ggplotify/index.html) and [cowplot](https://cran.r-project.org/web/packages/cowplot/index.html).
You'll have to create two independent karyoplots ...
written 28 days ago by
bernatgel • 2.2k
2
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1
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132
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... Hi @mschmid,
You can create plots like the ones you ask with [karyoploteR]. It's not trivial, but it's doable.
The key is to define a custom genome with a single chromosome "Cust" going from 1 to the length of the sequence, and then plot the sequence and the bed files on it.
I have created an ex ...
written 5 weeks ago by
bernatgel • 2.2k
1
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0
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Comment:
C: snp density plot
... Does it work for you to add a ruler with the size in megabases?
For that simply use `kpAddBaseNumbers(kp)` (more information in [the tutorial](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/BaseNumbersAndBandNames/BaseNumbersAndBandNames.html))
...
written 5 weeks ago by
bernatgel • 2.2k
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245
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Comment:
C: snp density plot
... Great :)
Glad it worked. I'm concerned that it should have worked with the other code too... would it be possible and feasible to send me the actual data file (or at least a small part (the first 100 lines if it fails with only 100 lines)) to check what's going on? my email is bgel@igtp.cat ...
written 5 weeks ago by
bernatgel • 2.2k
1
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0
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245
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0
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Comment:
C: snp density plot
... Oook... that's strange.
What about `all(is.numeric(vars[,2]))`?
Maybe you can try directly
vars <- GenomicRanges::GRanges(seqnames=vars[,1], ranges=IRanges::IRanges(start=vars[,2], end=vars[,2))
and see if it works. But somehow, not all your POS are valid numbers for GRanges...
...
written 5 weeks ago by
bernatgel • 2.2k
0
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0
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245
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Comment:
C: snp density plot
... Hmm...
The example data you provided is the actual first few lines of your data file? The error is telling you that in some lines of the file POS is not a number. Might it be that there are some NA's in POS? What's the result of
any(is.na(vars[,2]))
...
written 5 weeks ago by
bernatgel • 2.2k
2
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0
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245
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0
answers
Comment:
C: snp density plot
... Hi evelyn,
Ok,let me see if I understand this correctly :) you have information of the same SNPs for all samples, so for all your samples the position and density of the SNPs will be exactly the same.
If you want a single plot with the position (only a few SNPs) or density (if you have many) of t ...
written 6 weeks ago by
bernatgel • 2.2k
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