Package 'WormTensor' reference manual

Title:	A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'
Description:	A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.
Authors:	Kentaro Yamamoto [aut, cre], Koki Tsuyuzaki [aut], Itoshi Nikaido [aut]
Maintainer:	Kentaro Yamamoto <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.1
Built:	2024-10-28 05:38:22 UTC
Source:	https://github.com/rikenbit/wormtensor

Components for WormTensor object

Description

These are generic methods for WormTensor

Usage

worm_membership(object, k)

worm_clustering(
  object,
  algorithm = c("MCMI", "OINDSCAL", "CSPA"),
  num.iter = 30,
  thr = 1e-10,
  verbose = FALSE
)

worm_evaluate(object, labels = NULL)

worm_visualize(
  object,
  out.dir = tempdir(),
  algorithm = c("tSNE", "UMAP"),
  seed = 1234,
  tsne.dims = 2,
  tsne.perplexity = 15,
  tsne.verbose = FALSE,
  tsne.max_iter = 1000,
  umap.n_neighbors = 15,
  umap.n_components = 2,
  silhouette.summary = FALSE
)
worm_membership(object, k)

worm_clustering(
  object,
  algorithm = c("MCMI", "OINDSCAL", "CSPA"),
  num.iter = 30,
  thr = 1e-10,
  verbose = FALSE
)

worm_evaluate(object, labels = NULL)

worm_visualize(
  object,
  out.dir = tempdir(),
  algorithm = c("tSNE", "UMAP"),
  seed = 1234,
  tsne.dims = 2,
  tsne.perplexity = 15,
  tsne.verbose = FALSE,
  tsne.max_iter = 1000,
  umap.n_neighbors = 15,
  umap.n_components = 2,
  silhouette.summary = FALSE
)

Arguments

`object`	WormTensor object
`k`	Assumed number of clusters
`algorithm`	Dimensional reduction methods
`num.iter`	The upper limit of iterations (Default value is 30)
`thr`	The lower limit of relative change in estimates (Default value is 1E-10)
`verbose`	Control message
`labels`	Labels for external evaluation
`out.dir`	Output directory (default: tempdir())
`seed`	Arguments passed to set.seed (default: 1234)
`tsne.dims`	Output dimensionality (default: 2)
`tsne.perplexity`	Perplexity paramete (default: 15)
`tsne.verbose`	logical; Whether progress updates should be printed (default: TRUE)
`tsne.max_iter`	The number of iterations (default: 1000)
`umap.n_neighbors`	The size of local neighborhood (default: 15)
`umap.n_components`	The dimension of the space to embed into (default: 2)
`silhouette.summary`	logical; If true a summary of cluster silhouettes are printed.

Generates WormTensor object A WormTensor object is generated from distance matrices.

Description

Generates WormTensor object A WormTensor object is generated from distance matrices.

Usage

as_worm_tensor(Ds)
as_worm_tensor(Ds)

Arguments

`Ds`	A list containing distance matrices

Value

An object containing distance matrices and metadata

Examples


    worm_download("mSBD", qc = "PASS")$Ds |> as_worm_tensor() -> object

worm_download("mSBD", qc = "PASS")$Ds |> as_worm_tensor() -> object

Generates clustering result A clustering result is generated from a membership tensor.

Description

Generates clustering result A clustering result is generated from a membership tensor.

Usage

## S4 method for signature 'WormTensor'
worm_clustering(
  object,
  algorithm = c("MCMI", "OINDSCAL", "CSPA"),
  num.iter = 30,
  thr = 1e-10,
  verbose = FALSE
)
## S4 method for signature 'WormTensor'
worm_clustering(
  object,
  algorithm = c("MCMI", "OINDSCAL", "CSPA"),
  num.iter = 30,
  thr = 1e-10,
  verbose = FALSE
)

Arguments

`object`	WormTensor object with a membership tensor
`algorithm`	Clustering methods
`num.iter`	The upper limit of iterations (Default value is 30)
`thr`	The lower limit of relative change in estimates (Default value is 1E-10)
`verbose`	Control message

Value

WormTensor object with a clustering result added

Examples


    # Pipe Operation
    worm_download("Euclid", qc = "WARN")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) -> object
    worm_clustering(object, verbose = TRUE) -> ob_mcmi
    worm_clustering(object, algorithm = "OINDSCAL", verbose = TRUE) -> ob_oind
    worm_clustering(object, algorithm = "CSPA", verbose = TRUE) -> ob_cspa

# Pipe Operation
    worm_download("Euclid", qc = "WARN")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) -> object
    worm_clustering(object, verbose = TRUE) -> ob_mcmi
    worm_clustering(object, algorithm = "OINDSCAL", verbose = TRUE) -> ob_oind
    worm_clustering(object, algorithm = "CSPA", verbose = TRUE) -> ob_cspa

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

Arguments

`data`	Time-series matrices
`distance`	"mSBD" or "SBD" or "Euclid" can be specified. mSBD means modified Shape-based distance.

Value

A list containing distance matrices

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")
# 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")

Downloads distance matrices 28 animals' data including 24 normal and 4 noisy are retrieved from figshare.

Description

Downloads distance matrices 28 animals' data including 24 normal and 4 noisy are retrieved from figshare.

Usage

worm_download(distance = c("mSBD", "Euclid"), qc = c("PASS", "WARN", "FAIL"))
worm_download(distance = c("mSBD", "Euclid"), qc = c("PASS", "WARN", "FAIL"))

Arguments

`distance`	"mSBD" or "Euclid" can be specified
`qc`	"PASS" or "WARN" or "FAIL" can be specified. "PASS" downloads 24 data except 4 noisy data. "WARN" downloads 27 data except 1 noisy data. "FAIL" downloads all 28 data.

Value

A List of containing distance matrices. The list also includes metadata for each animals.

Examples


    Ds_Euclid <- worm_download("Euclid", qc = "WARN")
    Ds_mSBD <- worm_download("mSBD", qc = "PASS")

Ds_Euclid <- worm_download("Euclid", qc = "WARN")
    Ds_mSBD <- worm_download("mSBD", qc = "PASS")

Evaluates clustering result An evaluation result is generated from a WormTensor object.

Description

Evaluates clustering result An evaluation result is generated from a WormTensor object.

Usage

## S4 method for signature 'WormTensor'
worm_evaluate(object, labels = NULL)
## S4 method for signature 'WormTensor'
worm_evaluate(object, labels = NULL)

Arguments

`object`	WormTensor object with a result of worm_clustering
`labels`	Labels for external evaluation

Value

WormTensor object with an evaluation result added

Examples


    # Pipe Operation
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() -> object
     # Internal evaluation
     worm_evaluate(object) -> object_internal

     # External evaluation by sample labels
     labels <- list(
         label1 = sample(3, length(object@clustering), replace = TRUE),
         label2 = sample(4, length(object@clustering), replace = TRUE),
         label3 = sample(5, length(object@clustering), replace = TRUE)
     )
     worm_evaluate(object, labels) -> object_external

     # External evaluation by worm_download labels
     Ds_mSBD <- worm_download("mSBD", qc = "PASS")
     labels <- list(
         label1 = replace(
             Ds_mSBD$labels$Class,
             which(is.na(Ds_mSBD$labels$Class)),
             "NA"
         ),
         label2 = sample(4, length(object@clustering), replace = TRUE),
         label3 = sample(5, length(object@clustering), replace = TRUE)
     )
     worm_evaluate(object, labels) -> object_external_Class

# Pipe Operation
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() -> object
     # Internal evaluation
     worm_evaluate(object) -> object_internal

     # External evaluation by sample labels
     labels <- list(
         label1 = sample(3, length(object@clustering), replace = TRUE),
         label2 = sample(4, length(object@clustering), replace = TRUE),
         label3 = sample(5, length(object@clustering), replace = TRUE)
     )
     worm_evaluate(object, labels) -> object_external

     # External evaluation by worm_download labels
     Ds_mSBD <- worm_download("mSBD", qc = "PASS")
     labels <- list(
         label1 = replace(
             Ds_mSBD$labels$Class,
             which(is.na(Ds_mSBD$labels$Class)),
             "NA"
         ),
         label2 = sample(4, length(object@clustering), replace = TRUE),
         label3 = sample(5, length(object@clustering), replace = TRUE)
     )
     worm_evaluate(object, labels) -> object_external_Class

Generates membership tensor A membership tensor is generated from distance matrices.

Description

Generates membership tensor A membership tensor is generated from distance matrices.

Usage

## S4 method for signature 'WormTensor'
worm_membership(object, k)
## S4 method for signature 'WormTensor'
worm_membership(object, k)

Arguments

`object`	WormTensor object with distance matrices
`k`	Assumed number of clusters

Value

WormTensor object with membership tensor added

Examples


    # Pipe Operation
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() -> object
    # k=6
    worm_membership(object, k = 6) -> object_k6

# Pipe Operation
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() -> object
    # k=6
    worm_membership(object, k = 6) -> object_k6

Plots evaluation result A visualization result is generated from a WormTensor object.

Description

Plots evaluation result A visualization result is generated from a WormTensor object.

Usage

## S4 method for signature 'WormTensor'
worm_visualize(
  object,
  out.dir = tempdir(),
  algorithm = c("tSNE", "UMAP"),
  seed = 1234,
  tsne.dims = 2,
  tsne.perplexity = 15,
  tsne.verbose = FALSE,
  tsne.max_iter = 1000,
  umap.n_neighbors = 15,
  umap.n_components = 2,
  silhouette.summary = FALSE
)
## S4 method for signature 'WormTensor'
worm_visualize(
  object,
  out.dir = tempdir(),
  algorithm = c("tSNE", "UMAP"),
  seed = 1234,
  tsne.dims = 2,
  tsne.perplexity = 15,
  tsne.verbose = FALSE,
  tsne.max_iter = 1000,
  umap.n_neighbors = 15,
  umap.n_components = 2,
  silhouette.summary = FALSE
)

Arguments

`object`	WormTensor object with a result of worm_evaluate
`out.dir`	Output directory (default: tempdir())
`algorithm`	Dimensional reduction methods
`seed`	Arguments passed to set.seed (default: 1234)
`tsne.dims`	Output dimensionality (default: 2)
`tsne.perplexity`	Perplexity parameter (default: 15)
`tsne.verbose`	logical; Whether progress updates should be printed (default: TRUE)
`tsne.max_iter`	Number of iterations (default: 1000)
`umap.n_neighbors`	The size of the local neighborhood (default: 15)
`umap.n_components`	The dimension of the space to embed into (default: 2)
`silhouette.summary`	logical; If true a summary of cluster silhouettes are printed.

Value

Silhouette plots. ARI with a merge result and each animal(with MCMI). Dimensional reduction plots colored by cluster, no. of identified cells, consistency(with labels), Class_label(with labels).

References

The .dist_nn function is quoted from dist_nn (not exported function) in package uwot(https://github.com/jlmelville/uwot/tree/f467185c8cbcd158feb60dde608c9da153ed10d7).

Examples


    # Temporary directory to save figures
    out.dir <- tempdir()

    # Labels
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() -> object
    Ds_mSBD <- worm_download("mSBD", qc = "PASS")
    labels <- list(
        label1 = replace(
            Ds_mSBD$labels$Class,
            which(is.na(Ds_mSBD$labels$Class)),
            "NA"
        ),
        label2 = sample(4, length(object@clustering), replace = TRUE),
        label3 = sample(5, length(object@clustering), replace = TRUE)
    )

    # Pipe Operation (without Labels)
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() |>
                    worm_evaluate() |>
                        worm_visualize(out.dir) -> object_no_labels

    # Pipe Operation (with Labels)
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() |>
                    worm_evaluate(labels) |>
                        worm_visualize(out.dir) -> object_labels

# Temporary directory to save figures
    out.dir <- tempdir()

    # Labels
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() -> object
    Ds_mSBD <- worm_download("mSBD", qc = "PASS")
    labels <- list(
        label1 = replace(
            Ds_mSBD$labels$Class,
            which(is.na(Ds_mSBD$labels$Class)),
            "NA"
        ),
        label2 = sample(4, length(object@clustering), replace = TRUE),
        label3 = sample(5, length(object@clustering), replace = TRUE)
    )

    # Pipe Operation (without Labels)
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() |>
                    worm_evaluate() |>
                        worm_visualize(out.dir) -> object_no_labels

    # Pipe Operation (with Labels)
    worm_download("mSBD", qc = "PASS")$Ds |>
        as_worm_tensor() |>
            worm_membership(k = 6) |>
                worm_clustering() |>
                    worm_evaluate(labels) |>
                        worm_visualize(out.dir) -> object_labels

S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R

Description

S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R

Slots

dist_matrices: list
n_animals: numeric
union_cellnames: character
n_union_cells: numeric
membership_tensor: Tensor
k: numeric
clustering_algorithm: character
clustering: numeric
weight: numeric
factor: matrix
consensus: matrix
eval: list
dimension_reduction_algorithm: character

Package 'WormTensor'

Help Index

Components for WormTensor object

Description

Usage

Arguments

Generates WormTensor object A WormTensor object is generated from distance matrices.

Description

Usage

Arguments

Value

Examples

Generates clustering result A clustering result is generated from a membership tensor.

Description

Usage

Arguments

Value

Examples

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

Description

Usage

Arguments

Value

Examples

Downloads distance matrices 28 animals' data including 24 normal and 4 noisy are retrieved from figshare.

Description

Usage

Arguments

Value

Examples

Evaluates clustering result An evaluation result is generated from a WormTensor object.

Description

Usage

Arguments

Value

Examples

Generates membership tensor A membership tensor is generated from distance matrices.

Description

Usage

Arguments

Value

Examples

Plots evaluation result A visualization result is generated from a WormTensor object.

Description

Usage

Arguments

Value

References

Examples

S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R

Description

Slots