doLeidenSubCluster

doLeidenSubCluster

Description

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

Usage

doLeidenSubCluster(
  gobject,
  name = "sub_pleiden_clus",
  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 = 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

name

name for new clustering result

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 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 genes

    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>`_