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lawremi / ggbio

Grid and ggplot2 based visualization for biological data
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Vignette Conversion Request #166

Open Rohit-Satyam opened 1 year ago

Rohit-Satyam commented 1 year ago

Hi, I'm volunteering with Sweave2Rmd and we're trying to convert all Bioconductor Sweave vignettes into Rmd files. Would you be willing to accept a pull request converting "ggbio: visualization toolkits for genomic data" for the "ggbio package" from one of our volunteers? We'll take care of converting the file. We'll ask you to review and accept the pull request. You'll also need to bump the version number in your DESCRIPTION file so that the build machines will recognize that a new version is available.

Thanks for your time.

lawremi commented 1 year ago

I'm curious about the rationale for converting to Rmd. I couldn't find any on the Sweave2Rmd github page. Regardless, please be my guest. I'm not very familiar with Rmd, but I don't remember Sweave/Latex anymore either, so it's all the same ;)

Rohit-Satyam commented 1 year ago

Hi, you can know more about Sweave2Rmd project here: https://bioconductor.github.io/sweave2rmd/index.html

Rohit-Satyam commented 1 year ago

As maybe a future user of your package can I test and update the vignette with hg38 , new EnsDb.Hsapiens.v86 and TxDb.Hsapiens.UCSC.hg38.knownGene instead of hg19 and EnsDb.Hsapiens.v75 and TxDb.Hsapiens.UCSC.hg19.knownGene.

lawremi commented 1 year ago

That's fine with me. As I said though, that page does not explain why you are doing this. I'm just curious, and I think it would be generally worth while for your effort to communicate its motivations.

Rohit-Satyam commented 1 year ago

Hi @lawremi

Here is the rationale: https://docs.google.com/presentation/d/11PX1CWperCET_oDMM43KSTIhwsuTtuqAO1kgY7Pq96w/edit#slide=id.g168379e359d_0_5