perrin-isir / xomx Goto Github PK

Hello,

When using bokeh for plotting, there is no auto-scalling of the legend.
For example, only a subset of my 81 labels are listed in the legend in the UMAP plot below:

Bokeh does not provide an auto-scaling of the legend depending on the number of labels we are using (see open issues on git: bokeh/bokeh#3880). But there are workarounds like here.

Let me know what you think @perrin-isir, but ideally that would be nice to make all labels appear like this (from scanpy PCA plot):

Best,
Paul

GitHub can display ipynb files as well as md files. It might be useful to supply the ipynb files so that those who want to follow along with the tutorials can do so more easily. Just a suggestion, though. These look great!

Hi,

would it be possible to consider adding a legend whenever possible when using the plot2d function ?
A typical use-case would be to plot a umap embedding in which we know the associated labels for each sample (e.g. the tumor type). So in that case adata.obs["labels"] would be defined.

For interactive plots it is not totally necessary since we can eventually mouse over each sample (but it would still be useful). On the other hand, I would find it nearly compulsory for plots we save (save_dir is defined) as we lose this interaction possibility.

Best,
Paul