R/stability-based-parameter-assessment.R
plot_feature_stability_mb_facet.Rd
Display a facet of plots where each subpanel is associated with a feature set and illustrates the distribution of the most frequent partition over the UMAP embedding.
plot_feature_stability_mb_facet(
feature_object_list,
text_size = 5,
n_facet_cols = 3,
point_size = 0.3
)
An object or a concatenation of objects returned by the `get_feature_stability` method
The size of the cluster label
The number of facet's columns.
The size of the points displayed on the plot.
A ggplot2 object.
set.seed(2021)
# create an artificial expression matrix
expr_matrix = matrix(c(runif(100*10), runif(50*10, min = 5, max = 7)), nrow = 150, byrow = TRUE)
rownames(expr_matrix) = as.character(1:150)
colnames(expr_matrix) = paste("feature", 1:10)
feature_stability_result = get_feature_stability(data_matrix = t(expr_matrix),
feature_set = colnames(expr_matrix),
feature_type = "feature_name",
steps = c(5,10),
npcs = 2,
n_repetitions = 3,
algorithm = 1,
# the following parameters are used by the umap function and are not mandatory
n_neighbors = 3,
approx_pow = TRUE,
n_epochs = 0,
init = "random",
min_dist = 0.3)
plot_feature_stability_mb_facet(feature_stability_result)