Graph construction parameters - ECC facet

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, boxplot_width = 0.5)

Arguments

nn_ecs_object

An object or a concatenation of objects returned by the `get_nn_importance` method.

boxplot_width

Used for adjusting the width of the boxplots; the value will be passed to the `width` argument of the `ggplot2::geom_boxplot` method.

Value

A ggplot2 object.

Examples

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)