phys2 / belki Goto Github PK

Grouping logic in svg exports of visualization plots (and possibly other plots) is disadvantageous in a number of ways:

• Every single data point resides inside a a group (containing this single object). The styling is applied to the group and not to the object
• Same for the marker proteins, the graph lines, the text, etc.
• Countless (many thousands!) empty groups are present in the svg
• All these one-object-groups reside in one super group

This results in severe performance issues when trying to use Inkscape to modify t-sne plots where several thousand proteins are displayed. Regrouping operations can be impossible even with Inkscape graphic options reduced to a bare minimum (M1 MacBook Pro).
I suggest the following modifications:

• Style is applied to objects directly
• Objects of a same type (e.g, circles, plot lines, text) are grouped into one group. This relates well to the logical overlaying (text is in front of circles that are in front of plot lines)
• Empty groups should be removed from the svg

When trying to import a large number of markers, an error message tells me that belki is "Refusing to load too many (nnnn) markers".

Probably the limitation exists for performance and/or usability reasons. A look into the code reveals a hard limit of 500 markers.

In the first place, it would be convenient if the error message stated the actual limit. Something like "Refusing to load too many (nnnn) markers. Maximum is 500.". This way the user doesn't have to look up this value in the code.

But maybe the limit could be dealt with somewhat differently? I suggest to either

1. Remove the hard limit but ask the user is it's OK to continue despite potential issues (lag, apparent freezes, etc) if more than LIMIT markers are to be loaded

or

2. Keep the limit in place, load all markers up to LIMIT and inform the user about all three numbers: the limit, the number of markers present in the file and the number of markers that were not loaded.

or

3. Combine both and ask the user something like

   Warning

   You are about to load 2369 markers. Loading more than 500 markers may cause serious performance issues and is not recommended."

   [Load first 500 markers] [Load all markers] [Abort]

Some obvious problems render the app unusable in dark mode on macOS. See attached file: "Proteins under cursor" window not readable because font changes to white in dark mode. Same problem for icons (ie top left stay black where they should become white). The list probably goes on...