continuity_score {SaturnCoefficient} | R Documentation |
Function that calculates the continuity score of a UMAP dimensionality reduction
Description
Function that calculates the continuity score of a UMAP dimensionality reduction
Usage
continuity_score(original_matrix, umap_output_layout, VERBOSE)
Arguments
original_matrix |
input matrix |
umap_output_layout |
output matrix of UMAP applied to original_matrix |
VERBOSE |
prints some intermediate message to standard output or not |
Value
a real value containing the continuity score
Examples
this_nrows <- 200
this_ncols <- 100
this_min <- 0
this_max <- 10000
noise_random_matrix <- matrix(runif(n = this_nrows * this_ncols,
min = this_min, max = this_max), nrow = this_nrows)
input_matrix <- as.matrix(noise_random_matrix)
these_nearest_neighbors <- 15
this_min_dist <- 0.05
library("umap")
custom.settings <- umap::umap.defaults
custom.settings$"n_neighbors" <- these_nearest_neighbors
custom.settings$"min_dist" <- this_min_dist
x_umap <- umap::umap(input_matrix, config=custom.settings)
this_verbose <- FALSE
thisCon <- continuity_score(input_matrix, x_umap$"layout", this_verbose)
cat("continuity = ", thisCon, "\n", sep="")
[Package SaturnCoefficient version 1.3 Index]