GEX_lineage_trajectories: This is a function to infer single cell trajectories and...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

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

Description

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

Usage

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

try({
lineage_trajectories <- GEX_lineage_trajectories(Platypus::small_vgm[[2]],
 grouping = 'group_id',
 cluster.num = "3")
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.