flekschas / hipiler Goto Github PK

Currently Z is used for undo and the zoom modifier. This is not ideal.

Rendering is not the issue. Some parts of the data management seem to be too slow or there's a memory leak somewhere

Styles seem to be broken

Currently the one needs to reload HiPiler to try different dimensions, zoom-out-levels, and un-balanced snippets. This should be supported on the fly.

Some links:

• https://github.com/jupyter-widgets/ipywidgets
• https://kazuar.github.io/jupyter-widget-tutorial/

Might alleviate the need for #11

Display histograms of the arrange measures in the statistics panel

Hi there,

I've made a csv config file to view my own data based on the example but when I drag-and-drop I get a "could not load data" error on the right hand side and the left hand side just "Loading...". Drag-and-drop works fine with the example csv file, though.

For the server column, I've tried both "localhost" and my private IP. Either of these works for HiGlass config files for my local instance of HiGlass. Does this need the "//" prefix? I don't know why this is included in the example and it didn't seem to make a difference for me.

I used the tileset UUID from my local instance of HiGlass for the dataset column.

I am using a custom coordinate system, so maybe that's causing issues?

Should I create a full .json config file instead?

Any help would be appreciated!

Currently one cannot remove snippets from a pile. This needs to be supported.

Currently low quality bins are treated as zero but they should be excluded completely from the mean

It should be possible to export the location of the currently viewed including assigned colors and extra annotation

HiPiler can run on GitHub pages but we need a fixed endpoint with an example instance (maybe with Rao's GM12878 and K562)

Add a detail snippet view to the statistics panel with a translation from the colormap to the number of reads.

Also see here: https://www.khronos.org/webgl/wiki/HandlingHighDPI

Let the user store textual annotation in addition to colors

Currently previews are limited to a certain number but the actual height should be displayed

This would be a cool way to work with HiPiler

There could be an extra mode such that snippets can be arranges as the user wants them to

Currently navigating to a snippet is a bit tedious (highlighting and manual pan-zoom).

This should be possible automatically.

There is currently no place which describes the existing keyboard shortcuts.

They could even integrated as temporary overlays on the interface.

It would be useful to be able to combine multiple categorical identifiers to a new one for auto-piling (e.g., _groupA & _groupB == _groupC)

Log transformation should be possible for all measures when arranging

This is currently hard-coded. The user should be able to change that

The readme or wiki should contain instructions on how to configure HiPiler

Currently only one session per browser is supported. Once a user opens a new session, HiPiler should ask if the old session should be continued or if a new one should be started.

We probably need an upper limit for the number of session to avoid memory issues.

hipiler.higlass.io/#docs/ redirects to hipiler.higlass.io/docs/ and back to hipiler.higlass.io/#docs/

Use a flat Float32Array representation for faster operations and consistency or directly use a lib like glMatrix.

Currently highlighting is only supported in one way: snippets -> hg

The other way should be support as well. Maybe even with a context menu to go to the snippet.