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fmalmeida / easy_circos

easy_circos is a simple conda package that aims on rapidly and easily creating minimal circos configurations templates based on input data.
https://easy-circos.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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Addition of heatmap track #4

Open arunprasanna83 opened 8 months ago

arunprasanna83 commented 8 months ago

Dear Felipe, A nice and useful feature would be to add heatmap as a track. For example, one use it to show expression values as binary color for fold change (red or green in case of up or down) or as a dynamic color scale in case of expression value.

It follows the same chr, start, end, value

Below is the link for example in circos. circos_heatmap

Thanks in advance.

fmalmeida commented 8 months ago

Hi @arunprasanna83 , Thanks for the suggestion and I can definitely work on that. I just need to guarantee I understand the use case.

Would this feature be in a way that the user provide the expressions tsv (chr, start, end, value).

Like: plot_circos --expression_data user_file.tsv ?

arunprasanna83 commented 8 months ago

Hi @arunprasanna83 , Thanks for the suggestion and I can definitely work on that. I just need to guarantee I understand the use case.

Would this feature be in a way that the user provide the expressions tsv (chr, start, end, value).

Like: plot_circos --expression_data user_file.tsv ?

Yes absolutely! Ideally, it will be

gene, start, end, value

But the user can easily map the

chr, start, end, value

using gene co-ordinate information and supply it as custom tsv file. the values: In case of log2FC values will be both + and - (ex: +2, -1.5) . In case of expression values, it will be an integer starting from 0 to n.

Thanks.