kmeans_haystack_highD {singleCellHaystack}

Function for k-means clustering of genes according to their distribution in a higher-dimensional space.

Description

Function for k-means clustering of genes according to their distribution in a higher-dimensional space.

Usage

kmeans_haystack_highD(
  x,
  detection,
  genes,
  grid.coordinates = NULL,
  k,
  scale = TRUE,
  ...
)

Arguments

x

Coordinates of cells in a 2D or higher-dimensional space. Rows represent cells, columns the dimensions of the space.

detection

A logical matrix showing which genes (rows) are detected in which cells (columns)

genes

A set of genes (of the 'detection' data) which will be clustered.

grid.coordinates

Coordinates of grid points in the same space as 'x', to be used to estimate densities for clustering.

k

The number of clusters to return.

scale

whether to scale data.

...

Additional parameters which will be passed on to the kmeans function.

Value

An object of class kmeans, describing a clustering into 'k' clusters

Examples

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