runNearestNeighborClustering: Clustering with nearest neighbor search
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

runNearestNeighborClustering

R Documentation

Clustering with nearest neighbor search

Description

A wrapper around the RANN::nn2() function - nearest neighbor clustering.

Usage

runNearestNeighborClustering(
  object,
  n_pcs = NULL,
  k = 50,
  naming = "nn2_{priority}_{treetype}",
  searchtype = "priority",
  treetype = "bd",
  radius = 0,
  eps = 0,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`n_pcs`	Numeric value or `NULL`. If numeric, specifies the number of principal components to use. If `NULL`, all principal components are used (as computed with `runPCA()`).
`k`	The maximum number of nearest neighbours to compute. The default value is set to the smaller of the number of columnns in data.
`naming`	Character value. A glue expression for the new cluster variable name.
`searchtype`	See details
`treetype`	Character vector. Character vector specifying the standard 'kd' tree or a 'bd' (box-decomposition, AMNSW98) tree which may perform better for larger point sets.
`radius`	Radius of search for searchtype='radius'
`eps`	Error bound: default of 0.0 implies exact nearest neighbour search
`overwrite`	Logical value. Must be `TRUE` to allow overwriting.
`verbose`	Logical. If `TRUE`, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
`searchtypes`	Character value. Either 'priority', 'standard' or 'radius '. See details for more.

Details

Search types: priority visits cells in increasing order of distance from the query point, and hence, should converge more rapidly on the true nearest neighbour, but standard is usually faster for exact searches. radius only searches for neighbours within a specified radius of the point. If there are no neighbours then nn.idx will contain 0 and nn.dists will contain 1.340781e+154 for that point.