User: bernatgel
bernatgel • 710
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Posts by bernatgel
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Answer:
A: Add a legend to circos plot
... As far a I know, there is no functionality in Circos to add labels to tracks. We usually use an external program (Inskscape or similar) to add the labels when preparing the figure to publish.
Another option would be to use a text track with the track names, and try to position them as if they were ...
written 16 hours ago by
bernatgel • 710
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... I edited the original answer to include some code ...
written 17 hours ago by
bernatgel • 710
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... Hi nattzy94,
The data in the example is randomly created with `x <- 1:23*10e6` and `y <- rnorm(23, mean=0.5, sd=0.25)`. In your case you would probably read it from a file with the data about your snps (position and frequency). If you can paste here the first lines of your data file I can try ...
written 2 days ago by
bernatgel • 710
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... You can use [karyoploteR](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx346) to create a plot similar to a manhattan plot and using any genome.
To create such plot you should first create an empty plot following [these instructions](https://bernatgel.github.i ...
written 3 days ago by
bernatgel • 710
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... You can take a look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069701/
They use a custom approach to CNV calling from single cell data but they provide a good guide and access to code as supplemetary material. Not a full blown package, but it might be helpful. ...
written 7 days ago by
bernatgel • 710
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... Hi @ajaybioinfo,
It won't be exactly the same image, but you can get something similar with the R package [karyoploteR](http://bioconductor.org/packages/karyoploteR).
1 - You can create a genome.bed file with the length of your chromosomes and use it to create a plot as in the [Custom Genome](h ...
written 14 days ago by
bernatgel • 710
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... Answering after a few years, in case anyone comes to this question from google et al.
You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/) to plot almost anything on any genome. There are some examples in the [karyoploteR page](https://bernatgel.github.io/karyoploter_tutorial) i ...
written 23 days ago by
bernatgel • 710
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... Hi @khhgng
karyoploteR is only a plotting package and can not help you with the selection and manipulation of your data. If you your genes a in a GRanges object, I would recommend you using the [subsetByOverlaps](https://kasperdanielhansen.github.io/genbioconductor/html/GenomicRanges_GRanges_Usage. ...
written 4 weeks ago by
bernatgel • 710
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... If you can use R, you could use [regioneR]( http://bioconductor.org/packages/regioneR/)'s `createRandomRegions` function to do that.
The trick here is to create a mask by subtracting your regions from the whole genome. With that mask the function will select random regions in the only unmasked par ...
written 5 weeks ago by
bernatgel • 710
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... You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/) for that. It's a new R/Bioconductor package to plot data on the genome with lots of room for configuration.
With karyoploteR you start with an empty plot and keep adding new data iteratively. In your case, we'll use a for loop ...
written 5 weeks ago by
bernatgel • 710
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