register_partition_methods {cola} | R Documentation

## Register user-defined partitioning methods

### Description

Register user-defined partitioning methods

### Usage

    register_partition_methods(..., scale_method = c("z-score", "min-max", "none"))

### Arguments

`...` | A named list of functions.
`scale_method` | Normally, data matrix is scaled by rows before sent to the partition function. The default scaling is applied by `scale`. However, some partition functions may not accept negative values which are produced by `scale`. Here `scale_method` can be set to `min-max` which scales rows by `(x - min)/(max - min)`. Note here `scale_method` only means the method to scale rows. When `scale_rows` is set to `FALSE` in `consensus_partition` or `run_all_consensus_partition_methods`, there will be no row scaling when doing partitioning. The value for `scale_method` can be a vector if user specifies more than one partition function.

### Details

The user-defined function should accept at least two arguments. The first two arguments are the data matrix and the number of subgroups. The third optional argument should always be `...` so that parameters for the partition function can be passed by `partition_param` from `consensus_partition`. If users forget to add `...`, it is added internally.

The function should return a vector of partitions (or class labels) or an object which can be recognized by `cl_membership`.

The partition function should be applied on columns (Users should be careful with this because some R functions apply on rows and some R functions apply on columns). E.g. following is how we register `kmeans` partition method:

      register_partition_methods(
          kmeans = function(mat, k, ...) {
              # mat is transposed because kmeans() applies on rows
              kmeans(t(mat), centers = k, ...)$centers
          }
      )

The registered partitioning methods will be used as defaults in `run_all_consensus_partition_methods`.

To remove a partitioning method, use `remove_partition_methods`.

There are following default partitioning methods:

"hclust"

  hierarchcial clustering with Euclidean distance, later columns are partitioned by `cutree`. If users want to use another distance metric or clustering method, consider to register a new partitioning method. E.g. `register_partition_methods(hclust_cor = function(mat, k) cutree(hclust(as.dist(cor(mat)))))`.

"kmeans"

  by `kmeans`.

"skmeans"

  by `skmeans`.

"pam"

  by `pam`.

"mclust"

  by `Mclust`. mclust is applied to the first three principle components from rows.

Users can register two other pre-defined partitioning methods by `register_NMF` and `register_SOM`.

### Value

No value is returned.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### See Also

`all_partition_methods` lists all registered partitioning methods.

### Examples

    all_partition_methods()
    register_partition_methods(
        random = function(mat, k) sample(k, ncol(mat), replace = TRUE)
    )
    all_partition_methods()
    remove_partition_methods("random")

[Package cola version 1.4.1 Index]