select_partition_number-ConsensusPartition-method {cola} | R Documentation

## Several plots for determining the optimized number of subgroups

### Description

Several plots for determining the optimized number of subgroups

### Usage

    ## S4 method for signature 'ConsensusPartition'
    select_partition_number(object, mark_best = TRUE, all_stats = FALSE)

### Arguments

`object` | A `ConsensusPartition-class` object.
`mark_best` | Whether mark the best k in the plot.
`all_stats` | Whether to show all statistics that were calculated. Used internally.

### Details

There are following plots made:

- eCDF of the consensus matrix under each k, made by `plot_ecdf,ConsensusPartition-method`,

- `PAC` score,

- mean sihouette score,

- the `concordance` for each partition to the consensus partition,

- area increase of the area under the ECDF of consensus matrix with increasing k,

- Rand index for current k compared to k - 1,

- Jaccard coefficient for current k compared to k - 1,

### Value

No value is returned.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    data(golub_cola)
    select_partition_number(golub_cola["ATC", "skmeans"])

[Package cola version 1.8.1 Index]