hclust_haystack: Function for hierarchical clustering of genes according to...

In alexisvdb/singleCellHaystack: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space

Description

Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space

Usage

hclust_haystack(
  x,
  expression,
  grid.coordinates,
  hclust.method = "ward.D",
  cor.method = "spearman",
  ...
)

## S3 method for class 'matrix'
hclust_haystack(
  x,
  expression,
  grid.coordinates,
  hclust.method = "ward.D",
  cor.method = "spearman",
  ...
)

## S3 method for class 'data.frame'
hclust_haystack(
  x,
  expression,
  grid.coordinates,
  hclust.method = "ward.D",
  cor.method = "spearman",
  ...
)

Arguments

x	a matrix or other object from which coordinates of cells can be extracted.
expression	expression matrix.
grid.coordinates	coordinates of the grid points.
hclust.method	method used with hclust.
cor.method	method used with cor.
...	further parameters passed down to methods.

alexisvdb/singleCellHaystack documentation built on Jan. 17, 2024, 10:45 a.m.