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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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missing function for circos plot visualization #269

Closed cklee7 closed 1 month ago

cklee7 commented 1 month ago

Hi,

Thank you for this nice package! I would like to visualize my NicheNet output in a circos plot following this vignette https://github.com/saeyslab/nichenetr?tab=readme-ov-file#:~:text=Seurat%20Wrapper%20%2B%20circos%20visualization

but I ran into this error when I tried to run the assign_lignads_to_cell_type() function.

ligand_type_indication_df<-assign_ligands_to_cell_type(seuratobj, nichenet_output$top_ligands, celltype_col="cell_type") Error in assign_ligands_to_cell_type(seuratobj, nichenet_output$top_ligands, : could not find function "assign_ligands_to_cell_type

The current version of nichenetr I have is 2.1.0. I'm not sure how to proceed as I'm new to bioinformatics and still learning how to troubleshoot, I really appreciate your time and help in this matter!

csangara commented 1 month ago

Hi @cklee7,

It seems like there might be a typo - the function is named assign_ligands_to_celltype (there is no underscore between "cell" and "type"), can you try it again?

cklee7 commented 1 month ago

Hi, I restarted my session and found the function. Thanks so much!