WormTensor (version 0.1.2)

worm_distance: Generates distance matrices Distance matrices are generated between the cells of multiple animals (Caenorhabditis elegans) from time-series matrices.

Description

Generates distance matrices Distance matrices are generated between the cells of multiple animals (Caenorhabditis elegans) from time-series matrices.

Usage

worm_distance(data, distance = c("mSBD", "SBD", "Euclid"))

Value

A list containing distance matrices

Arguments

data

Time-series matrices

distance

"mSBD" or "SBD" or "Euclid" can be specified. mSBD means modified Shape-based distance.

Examples

# Toy data
n_cell_x <- 13
n_cell_y <- 24
n_cell_z <- 29
n_cells <- 30
n_time_frames <- 100

# 13 cells, 100 time frames
animal_x <- matrix(runif(n_cell_x * n_time_frames),
    nrow = n_cell_x, ncol = n_time_frames
)
rownames(animal_x) <- sample(seq(n_cells), n_cell_x)
colnames(animal_x) <- seq(n_time_frames)

# 24 cells, 100 time frames
animal_y <- matrix(runif(n_cell_y * n_time_frames),
    nrow = n_cell_y, ncol = n_time_frames
)
rownames(animal_y) <- sample(seq(n_cells), n_cell_y)
colnames(animal_y) <- seq(n_time_frames)

# 29 cells, 100 time frames
animal_z <- matrix(runif(n_cell_z * n_time_frames),
    nrow = n_cell_z, ncol = n_time_frames
)
rownames(animal_z) <- sample(seq(n_cells), n_cell_z)
colnames(animal_z) <- seq(n_time_frames)

# Positive Control of Difference between SBD and mSBD
animal_z[2, ] <- -animal_x[1, ]
X <- list(
    animal_x = animal_x,
    animal_y = animal_y,
    animal_z = animal_z
)
Ds_mSBD <- worm_distance(X, "mSBD")