Thank you for bringing TCR analyses together with transcriptome analyses with Platypus!
I encountered some errors when creating a vgm object with VDJ_GEX_matrix() after updating RStudio and Seurat.
The first error is associated with && evaluation of logical vectors in if() statement:
After googling, it seems to be related to the same problem as described here:https://github.com/rstudio/gt/issues/1004
After doing a perhaps inappropriate fix by changing && to & in line 1862 (VDJ.proc$Nr_of_VJ_chains == 0 & VDJ.proc$Nr_of_VDJ_chains), I was able to create the vgm object.
Another issue is with Seurat updated expression for UMAP_1 and UMAP_2. They are formatted as lowercase (i.e. "umap_1", "umap_2") in the latest Seurat version packageVersion("Seurat") ‘4.9.9.9049’ and therefore the umap components are not added to the vgm object when a Seurat object is fed to VDJ_GEM_matrix(). A quick but short-term change of "UMAP" to "umap" in VDJ_GEX_matrix() fixed the warning.
Hi,
Thank you for bringing TCR analyses together with transcriptome analyses with Platypus!
I encountered some errors when creating a vgm object with
VDJ_GEX_matrix()after updating RStudio and Seurat.After googling, it seems to be related to the same problem as described here:https://github.com/rstudio/gt/issues/1004 After doing a perhaps inappropriate fix by changing
&&to&in line 1862 (VDJ.proc$Nr_of_VJ_chains == 0 & VDJ.proc$Nr_of_VDJ_chains), I was able to create the vgm object.packageVersion("Seurat") ‘4.9.9.9049’and therefore the umap components are not added to the vgm object when a Seurat object is fed toVDJ_GEM_matrix(). A quick but short-term change of "UMAP" to "umap" inVDJ_GEX_matrix()fixed the warning.Jian