ViewPseudo: ViewPseudo

In zhongmicai/bigSCale2_singleCell: A framework for the analysis of single cell data (RNA-seq and ATAC-seq) including clustering,phenotyping,pseudotime and inferring gene regulatory networks.

Description

View the Pseudotime and colors the cell with different options

Usage

ViewPseudo(object, color.by, transform.in)

Arguments

color.by	clusters to color cell by the cluster of belonging. pseudo to color cell by the pseudotime. A gene name to color cell by its expression.
transform.in	adjustmet of gene expression for better visualuzation. Default is trim, you can use log to visualize log2(counts)+1
sce	object of the SingleCellExperiment class.

Examples

ViewPseudo(sce,'clusters')
ViewPseudo(sce,'pseudo')
ViewPseudo(sce,'Olig1')

zhongmicai/bigSCale2_singleCell documentation built on Nov. 5, 2019, 1:26 p.m.