Relationship Between Number of Nearest Neighbors and Graph Connectivity

Display the distribution of the number connected components obtained for each number of neighbors across random seeds.

plot_connected_comps_evolution(nn_conn_comps_object)

Arguments

nn_conn_comps_object

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

Value

A ggplot2 object with boxplots for the connected component distributions.

Note

The number of connected components is displayed on a logarithmic scale.

Examples

set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(c(runif(50*10), runif(50*10, min = 1, max = 2)), nrow = 100, byrow = TRUE)
rownames(expr_matrix) = as.character(1:100)

# the graph reduction type is PCA, so we can provide the expression matrix as argument
nn_conn_comps_obj = get_nn_conn_comps(object = expr_matrix,
    n_neigh_sequence = c(2,3,5),
    config_name = "example_config",
    n_repetitions = 10,
    graph_reduction_type = "PCA",
    transpose = FALSE,
    # the following parameter is used by the irlba function and is not mandatory
    nv = 3)
plot_connected_comps_evolution(nn_conn_comps_obj)
#> Warning: Transformation introduced infinite values in continuous y-axis