cds_trajectory_to_seurat: Copy a trajectory from a cell data set (cds) object to...

In Close-your-eyes/scexpr: Lots of helpers and wrappers to analyze scRNAseq data sets

Copy a trajectory from a cell data set (cds) object to respective the Misc slot of a Seurat object (SO)

Description

The code lines are copied from monocle3::plot_cells The aim is to have all data in a Seurat object to allow plot creation with a common style/layout.

Usage

cds_trajectory_to_seurat(
  cds,
  SO,
  x = 1,
  y = 2,
  reduction_method = "UMAP",
  name = "trajectory",
  pseudotime_metacol_name = "pseudotime"
)

Arguments

cds	a cell data set
SO	an Seurat object
x	column number of reduction_method to use as x-axis
y	column number of reduction_method to use as y-axis
reduction_method	name of reduction, currently only UMAP allows, according to monocle3
name	target slot name in Seurat::Misc; will be overwritten if already existing
pseudotime_metacol_name	name of new column in [e-mail] for pseudotime information; set to NULL to not add a column to meta.data of SO

Close-your-eyes/scexpr documentation built on April 21, 2023, 10:27 a.m.