collect_plots-ConsensusPartitionList-method: Collect plots from ConsensusPartitionList object

In jokergoo/cola: A Framework for Consensus Partitioning

Collect plots from ConsensusPartitionList object

Description

Collect plots from ConsensusPartitionList object

Usage

## S4 method for signature 'ConsensusPartitionList'
collect_plots(object, k = 2, fun = consensus_heatmap,
    top_value_method = object@top_value_method,
    partition_method = object@partition_method,
    verbose = TRUE, mc.cores = 1, cores = mc.cores, ...)

Arguments

object	A ConsensusPartitionList-class object from run_all_consensus_partition_methods.
k	Number of subgroups.
fun	Function used to generate plots. Valid functions are consensus_heatmap, plot_ecdf, membership_heatmap, get_signatures and dimension_reduction.
top_value_method	A vector of top-value methods.
partition_method	A vector of partitioning methods.
verbose	Whether to print message.
mc.cores	Number of cores. This argument will be removed in figure versions.
cores	Number of cores, or a cluster object returned by makeCluster.
...	other Arguments passed to corresponding fun.

Details

Plots for all combinations of top-value methods and parittioning methods are arranged in one single page.

This function makes it easy to directly compare results from multiple methods.

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

See Also

collect_plots,ConsensusPartition-method collects plots for a single ConsensusPartition-class object.

Examples

data(golub_cola)
collect_plots(cola_rl, k = 3)
collect_plots(cola_rl, k = 3, fun = membership_heatmap)
collect_plots(cola_rl, k = 3, fun = get_signatures)

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