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Add a custom feature similarity matrix to the mmo

AddCustomSim.Rd

Stores any user-supplied pairwise feature similarity matrix in the mmo so it can be used by GetBetaDiversity(), GetAlphaDiversity(), and HeatmapPlot() via the distance argument. Accepts either a dense numeric matrix or a sparse dgCMatrix (from the Matrix package).

Usage

AddCustomSim(mmo, sim_matrix, name)

Arguments

mmo

The mmo

sim_matrix

A square numeric matrix or sparse Matrix of pairwise feature similarities (see Details for format requirements).

name

A short string used to identify this matrix in downstream functions (e.g. "tanimoto", "npc"). Stored as mmo$<name>.sim and referenced via distance = "<name>". Must not conflict with built-in names: "dreams", "cosine", "m2ds".

Value

The mmo with the similarity matrix stored in mmo$<name>.sim.

Details

Required matrix format:

  • A square numeric matrix (or sparse dgCMatrix) with equal row and column names.

  • Row and column names must be feature IDs matching the id column in mmo$feature_data.

  • Values must be similarities in the range [0, 1], where 1 means identical and 0 means maximally different.

  • The diagonal should be 1 (a feature is identical to itself).

  • The matrix should be symmetric (sim[i,j] == sim[j,i]).

  • Features not present in mmo$feature_data are retained but silently ignored during analysis.

Examples

if (FALSE) {
# tanimoto_sim is a feature x feature similarity matrix from an external tool
mmo <- AddCustomSim(mmo, sim_matrix = tanimoto_sim, name = "tanimoto")
# Now use it anywhere a distance argument is accepted:
beta <- GetBetaDiversity(mmo, method = "CSCS", distance = "tanimoto")
alpha <- GetAlphaDiversity(mmo, mode = "weighted", distance = "tanimoto")
}