doLouvainSubCluster: doLouvainSubCluster

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

doLouvainSubCluster

Description

subcluster cells using a NN-network and the Louvain algorithm

Usage

doLouvainSubCluster(
  gobject,
  name = "sub_louvain_clus",
  version = c("community", "multinet"),
  cluster_column = NULL,
  selected_clusters = NULL,
  hvg_param = list(reverse_log_scale = T, difference_in_cov = 1, expression_values =
    "normalized"),
  hvg_min_perc_cells = 5,
  hvg_mean_expr_det = 1,
  use_all_genes_as_hvg = FALSE,
  min_nr_of_hvg = 5,
  pca_param = list(expression_values = "normalized", scale_unit = T),
  nn_param = list(dimensions_to_use = 1:20),
  k_neighbors = 10,
  resolution = 0.5,
  gamma = 1,
  omega = 1,
  python_path = NULL,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  return_gobject = TRUE,
  verbose = T
)

Arguments

gobject	giotto object
name	name for new clustering result
version	version of Louvain algorithm to use
cluster_column	cluster column to subcluster
selected_clusters	only do subclustering on these clusters
hvg_param	parameters for calculateHVG
hvg_min_perc_cells	threshold for detection in min percentage of cells
hvg_mean_expr_det	threshold for mean expression level in cells with detection
use_all_genes_as_hvg	forces all genes to be HVG and to be used as input for PCA
min_nr_of_hvg	minimum number of HVG, or all genes will be used as input for PCA
pca_param	parameters for runPCA
nn_param	parameters for parameters for createNearestNetwork
k_neighbors	number of k for createNearestNetwork
resolution	resolution for community algorithm
gamma	gamma
omega	omega
python_path	specify specific path to python if required
nn_network_to_use	type of NN network to use (kNN vs sNN)
network_name	name of NN network to use
return_gobject	boolean: return giotto object (default = TRUE)
verbose	verbose

Details

This function performs subclustering using the Louvain algorithm on selected clusters. The systematic steps are:

• 1. subset Giotto object

• 2. identify highly variable genes

• 3. run PCA

• 4. create nearest neighbouring network

• 5. do Louvain clustering

Value

giotto object with new subclusters appended to cell metadata

See Also

doLouvainCluster_multinet and doLouvainCluster_community

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.