sc3min_plot_consensus: Plot consensus matrix as a heatmap

In brickyyyy/MinimizedSC3: Minimized Single-Cell Consensus Clustering

Description

The consensus matrix is a NxN matrix, where N is the number of cells. It represents similarity between the cells based on the averaging of clustering results from all combinations of clustering parameters. Similarity 0 (blue) means that the two cells are always assigned to different clusters. In contrast, similarity 1 (red) means that the two cells are always assigned to the same cluster. The consensus matrix is clustered by hierarchical clustering and has a diagonal-block structure. Intuitively, the perfect clustering is achieved when all diagonal blocks are completely red and all off-diagonal elements are completely blue.

Usage

sc3min_plot_consensus.SingleCellExperiment(object, k, show_pdata)

## S4 method for signature 'SingleCellExperiment'
sc3min_plot_consensus(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

brickyyyy/MinimizedSC3 documentation built on May 23, 2019, 1:45 p.m.