Several plots for determining the optimized number of subgroups

Several plots for determining the optimized number of subgroups

# S4 method for 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

Zuguang Gu <z.gu@dkfz.de>

Examples

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