Generating neighbors matrix

[mhaist94]

Hi all,

thanks a lot for providing this awesome package. I ran into an issue when trying the generate the neighbors matrix using the create_neighborhood_matrix function (see below, the error message was referring to a missing or mismatched IO backend which i couldnt find in the doc so far). Loading of ark packages and importing the functions seemed to work fine. The dataframe i use has celltype label called "cell_types_mediumres", a unique region label called unique_region_num and a cellid called UID.

I wondered whether you ran into this issue before or whether you might have any advice on how to solve this error? I am running on a MacBook Pro M1 chip design. Thanks all!

[ngreenwald]

@alex-l-kong could you look into this when you have a chance?

[alex-l-kong]

@mhaist94 this issue usually arises when you try to load in a non-existent file or a non-.xr file. The first thing to check is to see that you're pointing to an existing dist_mat_dir. See what that variable in the notebook is set to, then navigate to that path on your computer. If it doesn't exist, or doesn't contain any .xr files, you'll need to run the distance matrix generation process first (a call to spatial_analysis_utils.calc_dist_matrix). The neighborhood analysis notebook should automatically generate this for you if you haven't run it yet.

[mhaist94]

Beautiful! Thank you Alex - really appreciate it - had to run the calc_dist_matrix function first and then it went through without issues. Best of thanks again!!