`subClusterCells`¶

subClusterCells

Description¶

subcluster cells

Usage¶

subClusterCells(
  gobject,
  name = "sub_clus",
  cluster_method = c("leiden", "louvain_community", "louvain_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 = 1,
  n_iterations = 1000,
  gamma = 1,
  omega = 1,
  python_path = NULL,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  return_gobject = TRUE,
  verbose = T
)

Arguments¶

Argument	Description
`gobject`	giotto object
`name`	name for new clustering result
`cluster_method`	clustering method 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
`n_iterations`	number of interations to run the Leiden 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 on selected clusters.: The systematic steps are:

1. subset Giotto object
1. identify highly variable genes
1. run PCA
1. create nearest neighbouring network
1. do clustering

Value¶

giotto object with new subclusters appended to cell metadata

Seealso¶

``doLouvainCluster_multinet` <#dolouvainclustermultinet>`_ , ``doLouvainCluster_community` <#dolouvainclustercommunity>`_: and @seealso ``doLeidenCluster` <#doleidencluster>`_