R/stability-based-parameter-assessment.R
plot_clustering_difference_facet.Rd
Display the distribution of the EC consistency for each clustering method and each resolution value on a given embedding The `all` field of the object returned by the `get_clustering_difference_object` method is used.
plot_clustering_difference_facet(
clustering_difference_object,
embedding,
low_limit = 0,
high_limit = 1,
grid = TRUE
)
An object returned by the `get_clustering_difference_object` method.
An embedding (only the first two dimensions will be used for visualization).
The lowest value of ECC that will be displayed on the embedding.
The highest value of ECC that will be displayed on the embedding.
Boolean value indicating whether the facet should be a grid (where each row is associated with a resolution value and each column with a clustering method) or a wrap.
A ggplot2 object.
set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(c(runif(250*10), runif(250*10, min = 5, max = 7)), nrow = 500)
rownames(expr_matrix) = as.character(1:500)
pca_embedding = irlba::irlba(expr_matrix, nv = 2)
pca_embedding = pca_embedding$u %*% diag(pca_embedding$d)
rownames(pca_embedding) = as.character(1:500)
adj_matrix = Seurat::FindNeighbors(pca_embedding,
k.param = 10,
nn.method = "rann",
verbose = FALSE,
compute.SNN = FALSE)$nn
clust_diff_obj = get_clustering_difference(graph_adjacency_matrix = adj_matrix,
resolution = c(0.5, 1),
n_repetitions = 10,
algorithm = 1:2,
verbose = FALSE)
plot_clustering_difference_facet(clust_diff_obj,pca_embedding)