Select Cells and Assign Identity

scSpotlight allows user to select cells of interest either by category (i.e. group.by) or manually via the lasso tool. After select cells, user will be able to assign new identity to them.

Select by category

After choosing “group.by” information from category module, all the identites of the grouping could be selected from a drop-down menu of the Rename Cluster module. For instance, here were illustrated pbmc3k dataset seurat_clusters groups, and overall expressions of the GNLY gene, which is a “Natrual Kill” (NK) cell marker. We found cluster 4 cells specifically express GNLY, thus could be assigned to NK cells. User could select cells of cluster 4 and input a new grouping name (e.g. celltype) in New Category Name, and assign cell labels “NK” in Assign As.

Unsupervised clustering result is not always perfect, and user may need to adjust cell annotation manually. One could activate lasso tools by pressing shift, then click and drag the mouse to select cells. The video below shows how to select cell of interest with lasso tool and assign new celltype labels.