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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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Track labels improvement #400

Open bluejay9676 opened 8 years ago

bluejay9676 commented 8 years ago
  1. Sometimes the name of the label is cut off.
  2. When there are tons of tracks, it's hard to tell which track is which on the east panel.

Number Label each track, and put track labels (like annotation) at the bottom of the window.

sa501428 commented 8 years ago

I don't think we should use numbers. We could try to do better truncation. Perhaps shorten the names to first whitespace encountered or first 5-6 characters? But I don't think any of our figures use numbers. And having the names is more intuitive there?

nchernia commented 8 years ago

I agree that numbers is confusing. The truncation isn't bad per se, and people can always rename their tracks. A legend would be great though, or maybe a tooltip with the full name

On Wed, Jun 22, 2016 at 1:56 PM, Muhammad Saad Shamim < notifications@github.com> wrote:

I don't think we should use numbers. We could try to do better truncation. Perhaps shorten the names to first whitespace encountered or first 5-6 characters? But I don't think any of our figures use numbers. And having the names is more intuitive there?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/theaidenlab/JuiceboxDev/issues/400#issuecomment-227825368, or mute the thread https://github.com/notifications/unsubscribe/ABWiWyxEUtLEK5R23o9YeWnW3bj7CeIqks5qOXdLgaJpZM4I8Bg0 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

nchernia commented 8 years ago

nevermind there's already the tooltip

On Wed, Jun 22, 2016 at 2:00 PM, Neva Durand neva@broadinstitute.org wrote:

I agree that numbers is confusing. The truncation isn't bad per se, and people can always rename their tracks. A legend would be great though, or maybe a tooltip with the full name

On Wed, Jun 22, 2016 at 1:56 PM, Muhammad Saad Shamim < notifications@github.com> wrote:

I don't think we should use numbers. We could try to do better truncation. Perhaps shorten the names to first whitespace encountered or first 5-6 characters? But I don't think any of our figures use numbers. And having the names is more intuitive there?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/theaidenlab/JuiceboxDev/issues/400#issuecomment-227825368, or mute the thread https://github.com/notifications/unsubscribe/ABWiWyxEUtLEK5R23o9YeWnW3bj7CeIqks5qOXdLgaJpZM4I8Bg0 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

bluejay9676 commented 8 years ago

Actually this one was from Erez, he thought it would be a little confusing for ppl to see which track is which (the vertical ones) if there are lots of tracks loaded. Pls share any ideas! Thanks!

nchernia commented 8 years ago

If lots of tracks are loaded, there's ample space for labels (since they appear on the y-axis as well and therefore make more empty horizontal space). Maybe load a bunch of tracks yourself and show him this.

On Wed, Jun 22, 2016 at 2:34 PM, bluejay9676 notifications@github.com wrote:

Actually this one was from Erez, he thought it would be a little confusing for ppl to see which track is which (the vertical ones) if there are lots of tracks loaded. Pls share any ideas! Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/theaidenlab/JuiceboxDev/issues/400#issuecomment-227836745, or mute the thread https://github.com/notifications/unsubscribe/ABWiWxrA-9mAMhd4Z_cjZAqSUACkYZ1aks5qOYA2gaJpZM4I8Bg0 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

bluejay9676 commented 8 years ago

I think what he wants is the vertical ones to be explicitly labeled just like horizontal ones.

One of the idea he suggested is to put label texts diagonally, so that both vertical and horizontal tracks are labeled. But then lack of space between tracks (GM12878 H4K20me1 for example in this image) won't be enough for such a long track name.

2016.06.21.14.19.17.HiCImage.pdf

nchernia commented 8 years ago

Oh I see - so numbers on the y-axis and then we can have a number next to the label up top?

Diagonally sounds nice too. Can we play with font size?

On Wed, Jun 22, 2016 at 3:07 PM, bluejay9676 notifications@github.com wrote:

I think what he wants is the vertical ones to be explicitly labeled just like horizontal ones.

One of the idea he suggested is to put label texts diagonally, so that both vertical and horizontal tracks are labeled. But then lack of space between tracks (GM12878 H4K20me1 for example in this image) won't be enough for such a long track name.

2016.06.21.14.19.17.HiCImage.pdf https://github.com/theaidenlab/JuiceboxDev/files/328569/2016.06.21.14.19.17.HiCImage.pdf

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/theaidenlab/JuiceboxDev/issues/400#issuecomment-227846173, or mute the thread https://github.com/notifications/unsubscribe/ABWiW4huRDizu6JTDEI-AZsTiFwZlU-vks5qOYgGgaJpZM4I8Bg0 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

sa501428 commented 8 years ago

Maybe coloring the text or having a colored square to the left of the label? Maybe this + a better job randomizing/assigning different colors? I'm worried that it'll get even more cluttered. Although I guess there is a lot of whitespace with large numbers of tracks

bluejay9676 commented 8 years ago

I will try options + suggestions made here and take a screenshot, and share to see which one is the best.

theaidenlab commented 8 years ago

I would suggest holding off on this. We have the much larger issue now of finding a good pdf export lib?

nchernia commented 8 years ago

Yes, true.

Muhammad could you get a quote for the commercial license just in case?

Jay, perhaps look into Postscript? It's pretty easy to convert from Postscript to PDF. You could also look into vector graphics exports.

All that nice work, this stinks. :(

On Thu, Jun 23, 2016 at 6:05 PM, Aiden Lab notifications@github.com wrote:

I would suggest holding off on this. We have the much larger issue now of finding a good pdf export lib?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/theaidenlab/JuiceboxDev/issues/400#issuecomment-228199492, or mute the thread https://github.com/notifications/unsubscribe/ABWiWz4tj4x2M7b7LqGP58HmSpNHoiFnks5qOwM7gaJpZM4I8Bg0 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

bluejay9676 commented 8 years ago

No problem. I'll get to it. Thanks!