R/stability-based-parameter-assessment.R
plot_n_neigh_k_correspondence.Rd
Display the distribution of the number of clusters obtained for each number of neighbors across random seeds.
plot_n_neigh_k_correspondence(nn_object_n_clusters)
An object or a concatenation of objects returned by the `get_nn_importance` method.
A ggplot2 object with the distributions displayed as boxplots.
The number of clusters is displayed on a logarithmic scale.
set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(runif(100*10), nrow = 100)
rownames(expr_matrix) = as.character(1:100)
nn_importance_obj = get_nn_importance(object = expr_matrix,
n_neigh_sequence = c(2,5),
n_repetitions = 5,
graph_reduction_type = "PCA",
algorithm = 1,
transpose = FALSE, # the matrix is already observations x features, so we won't transpose it
# the following parameter is used by the irlba function and is not mandatory
nv = 2)
plot_n_neigh_k_correspondence(nn_importance_obj)