doLeidenSubCluster#

Last Updated: Jan 29, 2024

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
1. identify highly variable fetures
1. run PCA
1. create nearest neighbouring network
1. do Leiden clustering

Value#

giotto object with new subclusters appended to cell metadata

See Also#

doLeidenCluster