UMAP plot

[Marcel-Salier]

For the UMAP we had before in the code of the notebook the way to delimit the heatmap, colormap and some other features like neighbours. Are we using scanpy right?

[fursham-h]

Sorry, I don't get what you mean by delimit. What do you want to do with the heatmap, colormap and neighbours?

[Marcel-Salier]

I don't think we show you that before. We set a color heatmap for a feature with a cut-off so the color change sits in the range that we see real biological changes. For instance we cutoff B3tub at 3 in the scale of 1 to 5 and we can see the color change in the range from 0 to 3 and 3 above is already max color, and the same we did with intensity products. Sounds better??

[fursham-h]

Okay I think I get what you mean. So for each cell, it can display a colour that represents 0,1,2 or 3 right?

[Marcel-Salier]

Yes, but kind of in a heatmap pattern.

[fursham-h]

Then I guess it's better to use plotting functions from ScanPy, as it is going to be inefficient to write wrappers for each type of ScanPy plots. We will, however, expose the fact that we are using a ScanPy object within our code.

We can replace obj.plotDim() with:

import scanpy as sc
sc.pl.umap(obj.adata)

We can then use any of the scanpy plotting functions from https://scanpy.readthedocs.io/en/stable/api.html#generic

[Marcel-Salier]

Yes, that's why I asked if we are using scanpy. So we can set some examples of what to plot.

[fursham-h]

Closing this issue, since we agreed on the implementation of scanpy plots