cellCyclePlot: cellCyclePlot

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

Computes cell cycle phase scores for each cell (based on the mean expression of phase markers from Whitfield et al, 2002). Plots a labelled tSNE plot from a Seurat object, where the clusters are labelled directly on the plot

Usage

cellCyclePlot(seurat, species = "m_musculus", facets = TRUE,
  legend = FALSE, return_scores = FALSE)

Arguments

seurat	Seurat object.
species	m_musculus or h_sapiens.
facets	Boolean to indicate whether a facet should be used for each cluster., or if all the clusters should be plotted together.
legend	Boolean to indicate whether legend should be included.

Value

A ggplot2 object. A tSNE plot with the cell cycle plots

Author(s)

Alexis Blanchet-Cohen

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.