doLeidenSubCluster: doLeidenSubCluster

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doLeidenSubCluster

Description

Further subcluster cells using a NN-network and the Leiden algorithm

Usage

doLeidenSubCluster(
  gobject,
  feat_type = NULL,
  name = "sub_pleiden_clus",
  cluster_column = NULL,
  selected_clusters = NULL,
  hvf_param = list(reverse_log_scale = TRUE, difference_in_cov = 1, expression_values =
    "normalized"),
  hvg_param = NULL,
  hvf_min_perc_cells = 5,
  hvg_min_perc_cells = NULL,
  hvf_mean_expr_det = 1,
  hvg_mean_expr_det = NULL,
  use_all_feats_as_hvf = FALSE,
  use_all_genes_as_hvg = NULL,
  min_nr_of_hvf = 5,
  min_nr_of_hvg = NULL,
  pca_param = list(expression_values = "normalized", scale_unit = TRUE),
  nn_param = list(dimensions_to_use = 1:20),
  k_neighbors = 10,
  resolution = 0.5,
  n_iterations = 500,
  python_path = NULL,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments

gobject	giotto object
feat_type	feature type
name	name for new clustering result
cluster_column	cluster column to subcluster
selected_clusters	only do subclustering on these clusters
hvf_param	parameters for calculateHVf
hvg_param	deprecatd, use hvf_param
hvf_min_perc_cells	threshold for detection in min percentage of cells
hvg_min_perc_cells	deprecated, use hvf_min_perc_cells
hvf_mean_expr_det	threshold for mean expression level in cells with detection
hvg_mean_expr_det	deprecated, use hvf_mean_expr_det
use_all_feats_as_hvf	forces all features to be HVF and to be used as input for PCA
use_all_genes_as_hvg	deprecated, use use_all_feats_as_hvf
min_nr_of_hvf	minimum number of HVF, or all features will be used as input for PCA
min_nr_of_hvg	deprecated, use min_nr_of_hvf
pca_param	parameters for runPCA
nn_param	parameters for parameters for createNearestNetwork
k_neighbors	number of k for createNearestNetwork
resolution	resolution of Leiden clustering
n_iterations	number of interations to run the Leiden algorithm.
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 Leiden algorithm on selected clusters. The systematic steps are:

• 1. subset Giotto object

• 2. identify highly variable fetures

• 3. run PCA

• 4. create nearest neighbouring network

• 5. do Leiden clustering

Value

giotto object with new subclusters appended to cell metadata

See Also

doLeidenCluster

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.