mk_dist_matrix function

Internal helper function to set up an (n m) x (n m) pairwise distance matrix for a plate with n rows and m columns

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 stats::dist()
• 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

Returns

The matrix with pairwise distances between any wells on the plate