sc3_plot_expression {SC3}R Documentation

Plot expression matrix used for SC3 clustering as a heatmap

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


[Package SC3 version 1.10.1 Index]