R: Graph construction parameters - ECC facet

plot_n_neigh_ecs {ClustAssess} | R Documentation

## Graph construction parameters - ECC facet

### Description

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.

### Usage

    plot_n_neigh_ecs(nn_ecs_object)

### Arguments

`nn_ecs_object` | An object or a concatenation of objects returned by the 'get_nn_importance' 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)

[Package ClustAssess version 0.3.0 Index]