`doLeidenSubCluster`¶

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 = T, 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 = T),
  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 = T
)

Arguments¶

Argument	Description
`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

Seealso¶

``doLeidenCluster` <#doleidencluster>`_