plot_n_neigh_ecs {ClustAssess} | R Documentation |
Display, for all configurations consisting in different number of neighbors, graph types and base embeddings, the EC Consistency of the partitions obtained over multiple runs on an UMAP embedding.
plot_n_neigh_ecs(nn_ecs_object)
nn_ecs_object |
An object or a concatenation of objects returned by the 'get_nn_importance' method. |
A ggplot2 object.
set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(c(runif(100*10), runif(100*10, min=5, max=6)), nrow = 200)
rownames(expr_matrix) = as.character(1:200)
nn_importance_obj = get_nn_importance(object = expr_matrix,
n_neigh_sequence = c(10,15,20),
n_repetitions = 10,
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_ecs(nn_importance_obj)