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MLWave avatar MLWave commented on May 17, 2024 2

Thanks for these issues.

  • I'll re-add graph_gravity and others to the new visualizations.
  • I'll update the documentation & examples
  • The older color function default was: distance to .min() of first dimension of projected_X. The new color function default is to color by row order of inverse_X. I think I liked the older default better.
  • average_signal_cluster was deprecated, and just passing the target labels to the color_function should do much of the same.
  • If your filter function output is 2D, and you want to use this for coloring, you have to somehow turn this into a 1D output. So you will likely lose some information. A crude way may be sum both outputs (df.color_function = df.tsne_1st_dim + df.tsne_2nd_dim)
  • The hard way to solve for above: split nodes in half and allow halves to be colored with two different colors (hard), the pragmatic way is allowing a 2D (n,m) array where n is number of rows and m are the different color function outputs. Then you can select these from a dropdown menu in the visualization. I'll begin work on this very soon. Something like:
html = mapper.visualize(graph,
    color_function=[[0,1],[2,3]],
    color_function_names=["target", "age"])

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sauln avatar sauln commented on May 17, 2024 1

All examples are up to date and running now in master.

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sauln avatar sauln commented on May 17, 2024

Some of these issues are addressed in PR #77

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