hclust_haystack_highD {singleCellHaystack}

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

Description

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

Usage

hclust_haystack_highD(
  x,
  detection,
  genes,
  method = "ward.D",
  grid.coordinates = NULL,
  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.

method

The method to use for hierarchical clustering. See '?hclust' for more information. Default: "ward.D".

grid.coordinates

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

scale

whether to scale data.

Value

An object of class hclust, describing a hierarchical clustering tree.

Examples

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