search

jokergoo / circlize

Circular visualization in R
http://jokergoo.github.io/circlize_book/book/
Other
959 stars 141 forks source link

Add an example of visualizing HiC dataset #137

Closed jokergoo closed 4 years ago

jezreel-me commented 4 years ago

What do you mean by HiC datasets? Highly Complex datasets?

I'm actually adjusting your package to summarize the multiple outputs of my multi-Omics code to study drug interactions. A couple limitations that I encounter when I use my HiC datasets with your package are:

  1. If your dataframe has a column with numeric values and NAs, you cannot plot the tracks, even if such column is not part of factors, x, region, y, or value. Temporary solution: Assign a value to the NAs using a function such as log2(1) to put 0s.
  2. If you're to use circlize to from expression datasets from any Omics to show differential expression between groups, you have to re-structure your datasets to assign x positions, and that sometimes gives irregular patterns for the links that look unintuitive.

I want to upload some examples if I understood what HiC meant. Please feel free to contact me or leave your email to see how we can collaborate for both my figures or want to hear my insights about using multi-Omics datasets with circlize.

Thanks,

Jezreel Pantaleon Garcia, MD (jezreel.me@gmail.com)

jokergoo commented 4 years ago

Hi, "HiC" is a technology which can measure the interactions between genomic regions. https://en.wikipedia.org/wiki/Chromosome_conformation_capture#Hi-C_(all-vs-all)

and a Hi-C heatmap looks like image

But never mind, thanks for your thought. I will move your suggestion to a new issue.

MichelMoser commented 4 years ago

Hi,

I would be super interested in circular Hi-C visualization and could contribute to code and testing.

Was this closed because you already have working examples?

Michel

jokergoo commented 4 years ago

No, I moved this discussion to #149

jokergoo commented 4 years ago

Hi, this is the circular HiC data visualization (the heatmap):

https://twitter.com/mpi_ie/status/1217364540305952769?s=20