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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Karyotype file of dual comparison error #325

Closed Hannah1746 closed 1 year ago

Hannah1746 commented 1 year ago

Hello.

I am trying to run:

require(RIdeogram) library(devtools)

karyotype <- read.table('karyotype.txt', header = T) synteny <- read.table('synteny.txt', header = T)

ideogram(karyotype = karyotype, synteny = synteny)

My files look like: karyotype.txt Chr Start End fill species size color Myx_Chr22 1 47849308 139b08 B 9.5 139b08 Myx_Chr43 1 38023304 139b08 B 9.5 139b08 Myx_Chr27 1 46332826 078dd8 A 9.5 078dd8 Myx_Chr42 1 38410338 078dd8 A 9.5 078dd8

synteny.txt Chr1 start1 end1 Chr2 start2 end2 22 14531668 14595454 27 32941637 32994325 22 14811096 15022136 27 32437958 32709008 22 15667970 15705569 27 31616867 31646678 ...

When I run this code I get this error:

Error in [<-.data.frame(*tmp*, i, 8, value = c(B = NAreal)) : new columns would leave holes after existing columns

I am just trying to understand what is going on.

Thank you for your time.

eweitz commented 1 year ago

Greetings! This repository is for Ideogram.js, a JavaScript library for chromosome visualization. Given your helpful example code, it seems you might be looking for RIdeogram.

That said, if the Ideogram.js synteny examples in the following are of interest to you, let me know!

ideogRam, the R wrapper for Ideogram.js, may well support those too.

Hannah1746 commented 1 year ago

Thank you for your fast response. I will reach out to RIdeogram about my error. I think I could also use the Genome alignment to get that same kind of figure I am looking for. Is there example code that I could use try this out?

eweitz commented 1 year ago

Yup! Source code for the genome alignment example is available at:

https://github.com/eweitz/ideogram/blob/gh-pages/genome-alignment.html

If you'd like, I can look into making a related visualization with your data. I'd just need your karyotype and synteny data attached or pasted in a comment here.