jiawen wang

Hi, what is "source" and target ? protein A (source) interacts with protein B(targets) protein B (source) interacts with protein A(targets) are they the same ? Does "source" corresponds to...

> hi @wangjiawen2013 , can you give me write access to your fork? I found the right line to fix it, you need to remove `sorted` from here: https://github.com/scverse/squidpy/blob/81b307d6e0696870125b1ccfc3a2fcff51b09b11/squidpy/gr/_ligrec.py#L388-L393 >...

please see scanpy tutorial: https://scanpy-tutorials.readthedocs.io/en/latest/spatial/integration-scanorama.html I think the [11] and [12] make the right cluster color. If I delete[11] and change the code[12] to the following, I think the color...

Thanks, I'll try it.

Figures size and position differed a lot when setting "img=False", it seems that sq.pl.spatial_scatter doesn't recognize scale_factor ?

According to the help (sq.pl.spatial_scatter): scale_factor Scaling factor used to map from coordinate space to pixel space. Found by default if ``library_id`` and ``img_key`` can be resolved. Otherwise, defaults to...

I don't know how to submit a PR. When setting "img=False", my picture looks good and the scale_factor is used, but when setting img as default, the figure is not...

Hi, I used the following code (there are four libraries in my anndata object, one library per batch): In [5]: adata.obs['batch'].value_counts() Out[5]: B1 16439 B2 13333 A1 10008 A2 10497...

It still didn't work, although I can run the example successfully. The four library of my anndata has different size and shape, did it cause the failure ? here is...

In [22]: adata = sc.read("scvi_integration/integration.h5ad") In [23]: sq.pl.spatial_scatter(adata,img=True,img_res_key="hires",library_id= ['A1', 'A2', 'B1', 'B2'],library_key='batch',color=['leiden']) In [24]: adata.uns['spatial'] Out[24]: {'A1': {'images': {'hires': array([[[1., 1., 1.], [1., 1., 1.], [1., 1., 1.], ..., [1.,...