dnjst

Variable grouping to `squidpy.pl.ligrec`

2

## Description (This is a suggestion/request; love the software) The dotplots output by `squidpy.pl.ligrec` are beautiful, but sometimes the number of ligand-receptor interactions can get unwieldy, and are not sorted...

fails indexing genomes with chromosome size >2^29-1

4

Hi thank you for the interesting looking program, I have been having an issue running it (latest singularity release) on an organism with a chromosome larger than the bai index...

Convert() fails on AnnData at metadata conversion step

1

I was using Convert() and it seems to fail on the step "Adding meta.features from var" with the following kind of error: ``` Error in dfile$obj_copy_from(src_loc = source, src_name =...

Multi-species cell type network plot

1

Hi, SAMap is great! I was wondering if there is a function, or code / short walkthrough you have shared somewhere or could share, to generate a plot like Figure...

get_mapping_scores() for cell types within same species non-zero

1

I was wondering, get_mapping_scores() returns a table of all pairwise scores between cell types of different species, but sets scores within the same species to zero. This may be a...

Additional metadata in results dataframe

2

Hi, I would really like a way to print the percent expression and CPM values for the (minimally expressed) ligand and receptor in the results dataframe for li.mt.rank_aggregate() or any...

Marsilea error in dc.plot_associations()

1

**Describe the bug** Hi, I'm following the tutorial for my own data and I get an error at the `dc.plot_associations()` step: `TypeError: ColormapRegistry.get_cmap() missing 1 required positional argument: 'cmap'` Is...

'coo_matrix' object has no attribute 'A'

3

Hi, during a step with the _filter_gnnm() function, I get the error `'coo_matrix' object has no attribute 'A'` I am using new scipy v1.14.0 which has deprecated the `.A` attribute....

Plot SVGs are massive in size due to color legend

2

**Describe the bug** I would like to make publication-quality editable figures of LIANA plots in SVG format, but am coming up an obstacle where the output SVG files are massive...

I did a simple find and replace of np.int with built-in python int This is described at https://numpy.org/devdocs/release/1.20.0-notes.html Note this: When replacing `np.int`, you may wish to use e.g. `np.int64`...