This is a function to infer single cell trajectories and identifying lineage structures on clustered cells. Using the slingshot library

GEX_lineage_trajectories(GEX, grouping, cluster.num)

Arguments

GEX: GEX output of the VDJ_GEX_matrix function (VDJ_GEX_matrix[[2]]))
grouping: Determine by which identifier to group by. E.g. 'group_id' or default 'seurat_clusters' which are automatically generated in the clustering process.
cluster.num: A seurat cluster number for starting point of the lineage. Can be identified by using Seurat::DimPlot(VGM[[2]],group.by = "seurat_clusters"). Default is "0".

Value

Returns a list. Element [[1]] returns updated GEX object with the inferred pseudotime trajectories per lineage. [[2]] returns the UMAP with the grouped cells. [[3]] and [[4]] show the slingshot inferred trajectories in two different styles.

Examples

if (FALSE) {
lineage_trajectories <- GEX_lineage_trajectories( VGM$GEX,
 grouping = 'group_id',
  cluster.num = "3")
}