mk_dist_matrix: Internal helper function to set up an (n m) x (n m) pairwise...
| mk_dist_matrix | R Documentation |
Internal helper function to set up an (n m) x (n m) pairwise distance matrix for a plate with n rows and m columns
Description
Internal helper function to set up an (n m) x (n m) pairwise distance matrix for a plate with n rows and m columns
Usage
mk_dist_matrix(
plate_x = 12,
plate_y = 8,
dist = "minkowski",
p = 2,
penalize_lines = "soft"
)
Arguments
plate_x |
Dimension of plate in x direction (i.e number of columns) |
plate_y |
Dimension of plate in y direction (i.e number of rows) |
dist |
Distance function as understood by |
p |
p parameter, used only if distance metric is 'minkowski'. Special cases: p=1 - Manhattan distance; p=2 - Euclidean distance |
penalize_lines |
How to penalize samples of the same group in one row or column of the plate. Valid options are: 'none' - there is no penalty and the pure distance metric counts, 'soft' - penalty will depend on the well distance within the shared plate row or column, 'hard' - samples in the same row/column will score a zero distance |
Value
The matrix with pairwise distances between any wells on the plate
