Results: Figure 5

[donovanr]

Issue summary

Fix up figure pretty significantly

Details

had not appreciated that there were only 23 cells with the Golgi tag in the paclitaxel-treated group. I think perhaps we should leave these out as it makes that class so imbalanced with respect to the others. Part B should show the marginal distributions as well as just the dots, and please label the damned axes (z1 and z2, I presume). Part D has way too many tiny, tiny images, and the conclusion is stepped on a bit by only walking from centroid to centroid. I think it would be better to take a slice across the whole distribution and walk from -4, -2 up to +4, +2 (i.e. along the same direction as the current traverse, but capturing both sides of the distribution). 7 images should be plenty. I don’t like using the “centroid distance from untreated” as a metric for statistical significance here in Part C, and the explanation given in the methods (lines 431-433) is wildly insufficient to understand what was done (also not a sentence). We really need some kind of measurement that compares the whole distribution. Let’s discuss alternatives. This is a place where truncation of the latent space to a smaller number of dimensions might offer better options for summary statistics (I think right now the “distance” is calculated in all dimensions, but please correct me if I’m wrong).

TODO

• code
• manuscript text
• figure

[donovanr]

@gregjohnso what do you think?

[donovanr]

need to re-sort the latent dims not by std(kld) but by mean(kld)