Inconsistent cell number in the json file and cell stats file

[zhanglab2008]

Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the zoom-in figure you showed in your Nature Biotech paper (figure3) is really amazing. I want to do the same with my own dataset. I have successfully read the json file and make the plot but the cell number in the json file is inconsistent with that in the cell_stats file. Appreciated if you can help or give comments... THanks!

[rocketeer1998]

Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the zoom-in figure you showed in your Nature Biotech paper (figure3) is really amazing. I want to do the same with my own dataset. I have successfully read the json file and make the plot but the cell number in the json file is inconsistent with that in the cell_stats file. Appreciated if you can help or give comments... THanks!

Hi @zhanglab2008 , could you give me some recommendations about plotting the GeoJson file, which is produced by save-polygons=geojson?

[zhanglab2008]

Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the zoom-in figure you showed in your Nature Biotech paper (figure3) is really amazing. I want to do the same with my own dataset. I have successfully read the json file and make the plot but the cell number in the json file is inconsistent with that in the cell_stats file. Appreciated if you can help or give comments... THanks!

Hi @zhanglab2008 , could you give me some recommendations about plotting the GeoJson file, which is produced by save-polygons=geojson?

I just used the json/geojson package in python and plot it out with matplotlib

[teng-gao]

I have the same question ..

[VPetukhov]

So, this is finally fixed in v0.6.0. Now the cell numbers are consistent, and you can use any plotting package for visualizing them.

[reillyeo]

The cell numbers are now consistent in that there are the same number of cells, but they still aren't ordered or labelled in the same way. Or am I missing something? Is it possible to relate a cell from the cell stats csv file to its polygon coordinates?