liana-py

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Update _tileplot.py for plotnine >=0.13

1

With `plotnine>=0.13` they changed the interface of `facet_grid` (see [Release notes](https://github.com/has2k1/plotnine/releases/tag/v0.13.0)); there's not more argument `facets` and doing something like [the tutorial](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html) ```python li.pl.tileplot(liana_res=lr_res, fill = 'expr', label='padj', label_fun =...

redst4r

Hi, and thanks for your tool. As exploring your tool, I came upon this LR_means, which I assume is the mean of the ligand and receptor means. But what can...

soniyalama

ValueError: Please check if appropriate organism/ID type was provided!

4

I get this error and it lists a number of genes that are not found in the data, although they are in var names (I checked). So I have no...

anke-king

Sanity check if liana uses the log normalised values

1

**Is your feature request related to a problem? Please describe.** Users sometimes run liana on raw or differently normalized/transformed data or forgets to set `use_raw=False` which results in `NaN` or...

ahmetrifaioglu

- Add a tutorial on GPU-accelerated misty - Plot the weighted views, currently stored in .obsm and .var of each extra view

dbdimitrov

Clarify LIANA + MOFA vignette

2

- pass `sample_key` explicitly - Make sure e.g. `samples_per_view` is a visible as a QC metric, and reduce it? - mention th `keep_stats` parameter - be explicit about `resource_name`

dbdimitrov

I should enforce a version for AnnData in the following updates w.r.t.: ```FutureWarning: The dtype argument is deprecated and will be removed in late 2024.```

dbdimitrov

MOFA talk with multiple samples

1

HI! First of all thanks for this great tool. I am trying to use LIANA to find CCC on a dataset with one condition but multiple samples. Thus, I am...

nicolebussola

dbdimitrov

Frequency Chord diagram and Heatmap in Python

7

Hi , Thanks a lot for this useful tool ! I'm running Liana and i'm curious that you cannot provide methods to generate Chord diagram or heatmap as in the...

maximelepetit