SpatialDM

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The process of 'Spatial Clustering of Local Spots' using SpatialDE is taking an excessive amount of time. Could I have overlooked some parameters?

2

I ran the 'Spatial Clustering of Local Spots' step using the following code: ```python from threadpoolctl import threadpool_limits with threadpool_limits(limits=10, user_api='blas'): results = SpatialDE.run(adata.obsm['spatial'], bin_spots.transpose()) histology_results, patterns = SpatialDE.aeh.spatial_patterns( adata.obsm['spatial'],...

ABU-TO

Bugs discovery for single-cell level spatialDM

5

Hi, I met a bug when inferring cci in image-based spatial data: ``` sdm.weight_matrix(adata, l=1.2, cutoff=0.2, single_cell=True) # weight_matrix by rbf kernel ```  Could you please take a look?...

HelloWorldLTY

I encountered an error when running sdm.extract_lr(adata, 'human', min_cell=3), following is the detailed issue: ``` sdm.weight_matrix(adata, l=1.2, cutoff=0.2, single_cell=False) # weight_matrix by rbf kernel ----> 3 sdm.extract_lr(adata, 'human', min_cell=3) #...

Smilenone

Code Update Request: Avoid 'np.float' Deprecation Error in melanoma.ipynb

3

Thank you for creating such a wonderful software! I immediately installed SpatialDM and tried running melanoma.ipynb, but I got an error. https://github.com/StatBiomed/SpatialDM/blob/main/tutorial/melanoma.ipynb Here is the code cell where the error...

yuifu

I keep getting error when running spatialdm_local AttributeError: 'NoneType' object has no attribute 'to_adata'

6

Hi, I followed the spatial dm example but I keep getting errors when running spatialdm_local. Below is the code I am running. ``` start = time.time() sdm.spatialdm_local(adata, n_perm=1000, method='both', specified_ind=None,...

smk5g5

Help with the simulations from the paper

2

Hi, Great paper and package. Thanks alot for making the code open source. I am trying to simulate the dataset for benchmarking cell-cell interaction tools following the Figure 1 f,g,h...

hiraksarkar

reading in h5ad file

1

Hi. I'm trying to read in a h5ad file which was generated from seurat R package. I am using this function: adata = sdm.read_spatialdm_h5ad(filename), but I get KeyError: 'geneInter'. Is...

anamaria-uofg

To avoid 'np.float' Deprecation Error in melanoma.ipynb https://github.com/StatBiomed/SpatialDM/issues/20

yuifu

weight_matrix with n_nearest_neighbors and n_neighbors

1

Hi, I am wondering why there are two parameters for nearest neighbours in weight matrix calculation. https://github.com/StatBiomed/SpatialDM/blob/aa1762496437a45787314a27e88313bdec6287c0/spatialdm/main.py#L34 It seems to me that there is no need for both or am...

wyq977

spatialdm_global does not work with a list of specified index, pair_selection_matrix would change adata

1

Hi I found out there's a bug in spatialdm_global https://github.com/StatBiomed/SpatialDM/blob/aa1762496437a45787314a27e88313bdec6287c0/spatialdm/main.py#L155 For example, if there are 400 lr pairs after `extract_lr`, one select 10 pairs for computation. User cannot specify specified_ind...

wyq977