SOM {FlowSOM} | R Documentation

## Build a self-organizing map

### Description

Build a self-organizing map

### Usage

    SOM(
      data,
      xdim = 10,
      ydim = 10,
      rlen = 10,
      mst = 1,
      alpha = c(0.05, 0.01),
      radius = stats::quantile(nhbrdist, 0.67) * c(1, 0),
      init = FALSE,
      initf = Initialize_KWSP,
      distf = 2,
      silent = FALSE,
      codes = NULL,
      importance = NULL
    )

### Arguments

`data` | Matrix containing the training data
`xdim` | Width of the grid
`ydim` | Hight of the grid
`rlen` | Number of times to loop over the training data for each MST
`mst` | Number of times to build an MST
`alpha` | Start and end learning rate
`radius` | Start and end radius
`init` | Initialize cluster centers in a non-random way
`initf` | Use the given initialization function if init == T (default: Initialize_KWSP)
`distf` | Distance function (1 = manhattan, 2 = euclidean, 3 = chebyshev, 4 = cosine)
`silent` | If FALSE, print status updates
`codes` | Cluster centers to start with
`importance` | array with numeric values. Parameters will be scaled according to importance

### Value

A list containing all parameter settings and results

### References

This code is strongly based on the `kohonen` package. R. Wehrens and L.M.C. Buydens, Self- and Super-organising Maps in R: the kohonen package J. Stat. Softw., 21(5), 2007

### See Also

`BuildSOM`

[Package FlowSOM version 2.2.0 Index]