Extract cellbin assignments of individual DNBs

[bmill3r]

Hello,

Is there a way to get the labels of the cellbins and the IDs or coordinates of the DNBs that were assigned to each cellbin in a cellbin GEF file? For example, in previous example data I have looked at (in this case, a GEM_CellBin.tsv.gz file), the matrix was something like:

A data.frame: 6 × 5
geneID  x   y   UMICount    label
<chr>   <int>   <int>   <int>   <dbl>
1   Gm26825 13476   11944   1   27298
2   Gm42418 13476   11944   1   27298
3   Pja1    8758    13656   1   37442
4   Cx3cl1  8758    13656   1   37442
5   Mgat3   11661   11611   1   25246
6   Gng3    5630    14950   1   44380

Where x and y are coordinates of the individual DNBs, and label is the cellbin each DNB was assigned to. Is it possible to extract something like this from the cellbin.gef file?

My goal is essentially to visualize the DNBs with respect to the different cellbins (ie, "cells") they were assigned to. Perhaps getting something like this:

Thanks, Brendan

[tanliwei-coder]

There are no DNBs infomation in cellbin GEF because it has already aggregated all DNBs to corresponding cellbins.

[bmill3r]

Hi @tanliwei-coder,

Ok thanks for letting me know!

Brendan