View source: R/LouvainDepart.R
LouvainDepart | R Documentation |
This function returns a list with elements useful to check and compare cell clustering.
LouvainDepart( data, pdat = NULL, PCA = TRUE, N = 15, pres = 0.8, tsne = FALSE, umap = FALSE, ... )
data |
A UMI count matrix with genes as rows and cells as columns or an S3 object for class 'scppp'. |
pdat |
A matrix used as input for cell clustering. If not specify, the departure matrix will be calculated within the function. |
PCA |
A logic value specifying whether apply PCA before Louvain clustering, default is |
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 logic value specifying whether t-SNE dimension reduction should be applied for visualization. |
umap |
A logic value specifying whether UMAP dimension reduction should be applied for visualization. |
... |
not used. |
This is a function used to get cell clustering using Louvain clustering algorithm implemented in the Seurat package.
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 tsne = FALSE
.
res_clust
: a data frame contains two columns: names (cell names) and clusters (cluster label)
Seuratscpoisson
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)
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