R: Relationship Between Number of Nearest Neighbors and Graph...

plot_connected_comps_evolution {ClustAssess} | R Documentation

## Relationship Between Number of Nearest Neighbors and Graph Connectivity

### Description

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

### Usage

    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)

[Package ClustAssess version 0.3.0 Index]