select_partition_number-ConsensusPartition-method: Several plots for determining the optimized number of...

In jokergoo/cola: A Framework for Consensus Partitioning

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 <[e-mail]>

Examples

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

jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.