doLeidenSubCluster#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L1321

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>`__