collect_plots-ConsensusPartitionList-method {cola} | R Documentation

## 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 <z.gu@dkfz.de>

### 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)

[Package cola version 1.8.1 Index]