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fjossinet / RNArtist

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
https://twitter.com/rnartist_app
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Zooming/base pairing probability/partition support #15

Open herber4 opened 2 years ago

herber4 commented 2 years ago

Hello RNArtist,

Love the visualization and looking forward to following this package as it grows.

Can you slow down the zoom in/out feature? if im not careful I can completely lose the molecule bc of how fast it zooms, haha.

Another question, are you planning on integrating the ability to visualize base pairing probability files?

Thanks,

Austin Herbert

herber4 commented 2 years ago

oh, and also a click and drag option to reposition the molecule on screen would be super cool!

fjossinet commented 1 year ago

Hi. Did you install the last version from this page: https://www.jdeploy.com/~rnartist

Could you give it a try because many things have been modified and fixed. Thanks

herber4 commented 1 year ago

Hello!

I have downloaded and am unable to load structures in databases with dot bracket and CT files generated from RNAstructure command line program.

here's the code I ran: Fold ANKHD1_chr5_140438044_140438944.fasta mfe.ct -md mfe.ct.txt 250 -mfe -sh ANKHD1_chr5_140438044_140438944_ANKHD1_chr5_140438044_140438944.shape

and the ct file I generated is attached (added .txt extension for GitHub to take)

looking forward to hearing back from you!

thanks

fjossinet commented 1 year ago

Hi!

Which version of RNArtist are you using? The "official" one with the installer or one you have package yourself from Github?

herber4 commented 1 year ago

Hello,

I have been using the version from this installer: https://www.jdeploy.com/~rnartist

I am on a Mac desktop, intel chip, Ventura v13.5.2 and I installed the MAcOS 10.14+

fjossinet commented 1 year ago

At now, everything is working fine for Vienna files only. But the nest release (very few days) will do the stuff for bpseq and ct. Meanwhile, I can send u a Vienna version of your data. Or the svg. Let me know.

fjossinet commented 1 year ago

Hi. I have released the new version (1.1.0). Give it a try and let me know. I was able to load your file mfe.ct in the bracket notation panel.

herber4 commented 1 year ago

looks great, looking forward to using this more often! thanks for the help :)

herber4 commented 1 year ago

hi,

I still think having a mode where we can click around the art, move the structure around with mouse. like when zoomed in on a structure being able to reposition the structure within that zoom by clicking and dragging with the mouse would be useful.

thanks!

fjossinet commented 1 year ago

You can translate the view with your mouse by keeping the right mouse button pressed and dragged. Concerning your request, I was thinking about the ability to define an area with the left button pressed and dragged to zoom in.

herber4 commented 1 year ago

yeah, that sounds like a great idea. We are working with experimental derived structures for introns, so it's nice to be able to rapidly move around the large structures. Also, being able to generate circular plots from a regular plot would be a cool function.