scpoisson (version 0.0.2)

LouvainDepart: Louvain clustering using departure as data representation

Description

This function returns a list with elements useful to check and compare cell clustering.

Usage

LouvainDepart(
  data,
  pdat = NULL,
  PCA = TRUE,
  N = 15,
  pres = 0.8,
  tsne = FALSE,
  umap = FALSE,
  ...
)
# S3 method for scppp
LouvainDepart(
  data,
  pdat = NULL,
  PCA = TRUE,
  N = 15,
  pres = 0.8,
  tsne = FALSE,
  umap = FALSE,
  ...
)
# S3 method for matrix
LouvainDepart(
  data,
  pdat = NULL,
  PCA = TRUE,
  N = 15,
  pres = 0.8,
  tsne = FALSE,
  umap = FALSE,
  ...
)

Value

A list with the following elements:

sdata

A Seurat object

tsne_data

A matrix containing t-SNE dimension reduction results, with cells as rows and first two t-SNE dimensions as columns; NULL if tsne = FALSE

umap_data

A matrix containing UMAP dimension reduction results, with cells as rows and first two UMAP dimensions as columns; NULL if umap = FALSE

res_clust

A data frame containing two columns: names (cell names) and clusters (cluster labels)

Arguments

data

A UMI count matrix with genes as rows and cells as columns, or an S3 object of class 'scppp'.

pdat

A matrix used as input for cell clustering. If not specified, the departure matrix will be calculated within the function.

PCA

A logical value specifying whether to apply PCA before Louvain clustering. Default is TRUE.

N

A numeric value specifying the number of principal components included for further clustering (default 15).

pres

A numeric value specifying the resolution parameter in Louvain clustering (default 0.8).

tsne

A logical value specifying whether t-SNE dimension reduction should be applied for visualization.

umap

A logical value specifying whether UMAP dimension reduction should be applied for visualization.

...

Not used.

Details

This is a function used to get cell clustering using Louvain clustering algorithm implemented in the Seurat package.

References

Seuratscpoisson

Examples

set.seed(1234)
test_set <- matrix(rpois(500, 2), nrow = 20)
rownames(test_set) <- paste0("gene", 1:nrow(test_set))
colnames(test_set) <- paste0("cell", 1:ncol(test_set))
LouvainDepart(test_set)