sc3_plot_consensus {SC3} | R Documentation

## Plot consensus matrix as a heatmap

### 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

    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

[Package SC3 version 1.16.0 Index]