preprocess_loom: Run Velocyto analysis on your Seurat2 object

In GrigoriiNos/rimmi.rnaseq: Set of functions for genomics data analysis

Run Velocyto analysis on your Seurat2 object

Description

This function allows you to preprocess loom file into the object that fits to plotting velocyto arrows on 2d embeddings

Usage

preprocess_loom(loom_path, Seurat_obj, emb)

Arguments

loom_path	path to the loom file, pre-calculated with python command line tool
Seurat_obj	Seurat object
emb	the matrix with 2d embeddings that you got from get_emb() function

Value

umap 2d plot with velocity

Examples

emb <- get_emb(B06, emb = 'umap')

rvel.cd <- preprocess_loom('~/Desktop/RIMMI/Adam_germinal_cenrte/B06/velocyto/B06.loom', B06, emb)

Seurat2_velocyto(rvel.cd, B06, emb)

GrigoriiNos/rimmi.rnaseq documentation built on April 29, 2022, 5:18 p.m.