sc3_plot_consensus: Plot consensus matrix as a heatmap

Description Usage Arguments

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

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sc3_plot_consensus.SingleCellExperiment(object, k, show_pdata)

## S4 method for signature 'SingleCellExperiment'
sc3_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


SC3 documentation built on May 2, 2018, 2:08 a.m.