Distance by Closeness — dist_by_closeness • EnrichedHeatmap

Distance by Closeness

dist_by_closeness(mat)

Arguments

mat: A numeric matrix where the distance is calculated by rows.

Details

For two rows in the matrix, assume x_1, x_2, ..., x_n1 are the column index of none-zero values in row 1 and y_1, y_2, ... y_n2 are the column index for non-zero values in row 2, the distance between the two rows based on the closeness is calculated as:


    d_closeness = sum_i sum_j(|x_i - y_j|) / (n_1*n_2)

Value

A dist object.

Author

Zuguang Gu <z.gu@dkfz.de>

Examples

x1 = c(0, 0, 0, 0, 1, 1, 1, 0, 0, 0)
x2 = c(0, 0, 0, 1, 1, 1, 0, 0, 0, 0)
x3 = c(1, 0, 0, 0, 1, 1, 0, 0, 0, 0)
m = rbind(x1, x2, x3)
dist(m)
#>          x1       x2
#> x2 1.414214         
#> x3 1.414214 1.414214
dist_by_closeness(m)
#>          1        2
#> 2 1.222222         
#> 3 2.222222 1.888889