Save in html or export the martix in mcool format

[baozg]

Hi, Alex

It's so nice to see tons of updates on ModDotPlot. I have a question about the interactive mode. For most plant genomes, its centromere/HOR region is unknown, it would be great to have an interactive mode to explore across the genome. But it would be difficult for most HPC to use with ssh port. So could the ModDotPlot have these features?

1. Save the output in plotly html format? It's easier to download and explore.
2. Similar to StainedGlass, could ModDotPlot save the raw matrix with cooler? It's easier to play around with HiGlass (identity, load annotation tracks, such as ChIP-Seq and gene/TE annotation)

Best regards
Zhigui

[alexsweeten]

Hi Zhigui,

Thanks for the suggesions! I've been working with supporting mcool and that functionality will be coming soon.

I'll also look into saving the plotly html, however since the interactive component requires Dash to compute a new distance matrix, this will lose a certain level of interactivity.

I'll ping this issue once these features are added!

[muffato]

Hi @alexsweeten. I've seen quite a few new releases for ModDotPlot. Did you have the chance to add cooler output support ?

Kind regards,
Matthieu

[BioOmics]

Dear @alexsweeten,

We also need this function. This is a very useful way to load the heatmap to jb2/igv/...

Kind regards
BioOmics

[alexsweeten]

Hi @muffato @BioOmics ,

I have included some very basic cooler output with the latest version of ModDotPlot (v0.9.6). In static mode, add the flag --cooler.

It would be great to get your feedback if this works for your needs! I'll leave this issue up for a little bit.

Best,
Alex