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GangCaoLab / CoolBox

Jupyter notebook based genomic data visualization toolkit.
https://gangcaolab.github.io/CoolBox/index.html
GNU General Public License v3.0
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Heatmap for tracks #93

Closed StarkTS98 closed 4 months ago

StarkTS98 commented 7 months ago

Hey, I am new to Coolbox and tried using it for my Bedgraph files. I am working with single-cell dataset where I have the bedgraph/bigwig files for each single cell. I can generate tracks for these but I was wondering if there is any way to create heatmaps of tracks instead of barcharts (similar to the heatmaps feature of IGV). I am wanting to generate something like this where each horizontal line is a single cell profile shown as a heatmap. This is a screenshot from igv but I want to use a command line based equivalent for reproducibility: image

Thanks in advance. If not by coolbox, is there any other command line based tool

Nanguage commented 7 months ago

Hello, this is achievable, but there is currently no built-in implementation. You can try customizing a Track like this yourself, I don't think it's difficult. For information on how to customize a Track, you can refer to here: https://gangcaolab.github.io/CoolBox/custom_elements.html