viewReduced: viewReduced

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 2D reduced dimentions. For the moment only supports TSNE.

Usage

viewReduced(object, color.by = "clusters", transform.in = "trim",
  method = "TSNE")

Arguments

color.by	clusters to color by clusters, or a gene name to color by gene names ( must be the names used in rownames(), or a factor to color by custom grouping.
transform.in	adjustmet of gene expression for better visualuzation. Default is trim, you can use log to visualize log2(counts)+1
method	can only be set to TSNE for the moment
sce	object of the SingleCellExperiment class.

Examples

viewReduced(sce,"clusters") # colors with clusters
viewReduced(sce,"Arx") # colors with Arx gene expression. The gene name must be same as in rownames()

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