sc3_plot_expression: Plot expression matrix used for SC3 clustering as a heatmap

In hemberg-lab/SC3: Single-Cell Consensus Clustering

Description

The expression panel represents the original input expression matrix (cells in columns and genes in rows) after the gene filter. Genes are clustered by kmeans with k = 100 (dendrogram on the left) and the heatmap represents the expression levels of the gene cluster centers after log2-scaling.

Usage

sc3_plot_expression.SingleCellExperiment(object, k, show_pdata)

## S4 method for signature 'SingleCellExperiment'
sc3_plot_expression(object, k,
  show_pdata = NULL)

Arguments

object	an object of 'SingleCellExperiment' class
k	number of clusters
show_pdata	a vector of colnames of the pData(object) table. Default is NULL. If not NULL will add pData annotations to the columns of the output matrix

hemberg-lab/SC3 documentation built on Dec. 18, 2019, 10:02 p.m.