Daniel Dimitrov
Daniel Dimitrov
PS. To implement `batch_key` wrt mean var + a new parameter for `var_min_nbatches`. + Add info to .var
Hi @dnjst, Indeed, this is purely on the plotnine side, but I found a way to rasterize the colour guide: ``` p2 = p + p9.guides(color=p9.guide_colorbar(display='raster', nbin=50)) p2.save('test2.pdf', dpi=300) ```...
Hi @maximelepetit, You should have that information in the `lr_res` - i.e. you can consider only the stats (e.g. logFC or p-values) of the ligand or receptor, rather than the...
Hi @Zach-Sten, Thanks for using LIANA+ and for the positive feedback. I realize we need to extend the plotting functions, and I will do my best to address at least...
Re volcano plot: you can check the volcano plot from decoupler in the meantime: https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html#Contrast-between-conditions I can also include it as an option in the liana+ tutorial
Hi @Zach-Sten, > I've been testing the use of cell2cell and MOFA within Liana and was wondering if there was a way to use the ligand-receptor information from the spatial...
Hi @Zach-Sten, > We have used NMF for getting our factors but were interested if other methods such as tenosr cell2cell and MOFA would give different results. Tensor-cell2cell uses a...
Perhaps via `requests_cache` or `pooch`
Or even better using the pypath https://github.com/saezlab/cache-manager
Hi @alecdavi, Is it possible to share a subset of your data? Or at least the code that you're running? Thanks! Daniel