R/stability-based-parameter-assessment.R
plot_clustering_difference_boxplot.Rd
Display EC consistency across clustering method and resolution values. The `filtered` field of the object returned by the `get_clustering_difference_object` method is used. Above each boxplot, the number of clusters is displayed.
plot_clustering_difference_boxplot(
clustering_difference_object,
text_size = 3,
dodge_width = 0.9,
boxplot_width = 0.4
)
An object returned by the `get_clustering_difference_object` method.
The size of the labels above boxplots.
Used for adjusting the horizontal position of the boxplot; the value will be passed to the `width` argument of the `ggplot2::position_dodge` method.
Used for adjusting the width of the boxplots; the value will be passed to the `width` argument of the `ggplot2::geom_boxplot` method.
A ggplot2 object with the EC consistency distributions. Higher consistency indicates a more stable clustering.
set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(runif(500*10), nrow = 500)
rownames(expr_matrix) = as.character(1:500)
adj_matrix = Seurat::FindNeighbors(expr_matrix,
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_boxplot(clust_diff_obj)