BatchContainer {designit}R Documentation

R6 Class representing a batch container.

Description

Describes container dimensions and samples to container location assignment.

Details

A typical workflow starts with creating a BatchContainer. Then samples can be assigned to locations in that container.

Public fields

trace

Optimization trace, a tibble::tibble()

Active bindings

scoring_f

Scoring functions used for optimization. Each scoring function should receive a BatchContainer. This function should return a floating point score value for the assignment. This a list of functions. Upon assignment a single function will be automatically converted to a list In the later case each function is called.

has_samples

Returns TRUE if BatchContainer has samples.

has_samples_attr

Returns TRUE if BatchContainer has sample atrributes assigned.

n_locations

Returns number of locations in a BatchContainer.

n_dimensions

Returns number of dimensions in a BatchContainer. This field cannot be assigned.

dimension_names

character vector with dimension names. This field cannot be assigned.

samples

Samples in the batch container. When assigning data.frame should not have column named .sample_id column.

samples_attr

Extra attributes of samples. If set, this is included into BatchContainer$get_samples() output.

assignment

Sample assignment vector. Should contain NAs for empty locations.

Assigning this field is deprecated, please use ⁠$move_samples()⁠ instead.

Methods

Public methods

Method new()

Create a new BatchContainer object.

Usage
BatchContainer$new(locations_table, dimensions, exclude = NULL)
Arguments
locations_table

A table with available locations.

dimensions

A vector or list of dimensions. Every dimension should have a name. Could be an integer vector of dimensions or a named list. Every value of a list could be either dimension size or parameters for BatchContainerDimension$new(). Can be used as an alternative to passing locations_table.

exclude

data.frame with excluded locations of a container. Only used together with dimensions.

Examples
bc <- BatchContainer$new(
  dimensions = list(
    "plate" = 3,
    "row" = list(values = letters[1:3]),
    "column" = list(values = c(1, 3))
  ),
  exclude = data.frame(plate = 1, row = "a", column = c(1, 3), stringsAsFactors = FALSE)
)

bc

Method get_samples()

Return table with samples and sample assignment.

Usage
BatchContainer$get_samples(
  assignment = TRUE,
  include_id = FALSE,
  remove_empty_locations = FALSE,
  as_tibble = TRUE
)
Arguments
assignment

Return sample assignment. If FALSE, only samples table is returned, with out batch assignment.

include_id

Keep .sample_id in the table. Use TRUE for lower overhead.

remove_empty_locations

Removes empty locations from the result tibble.

as_tibble

Return tibble. If FALSE returns data.table. This should have lower overhead, as internally there is a cached data.table.

Returns

table with samples and sample assignment.

Method get_locations()

Get a table with all the locations in a BatchContainer.

Usage
BatchContainer$get_locations()
Returns

A tibble with all the available locations.

Method move_samples()

Move samples between locations

This method can receive either src and dst or locations_assignment.

Usage
BatchContainer$move_samples(src, dst, location_assignment)
Arguments
src

integer vector of source locations

dst

integer vector of destination locations (the same length as src).

location_assignment

integer vector with location assignment. The length of the vector should match the number of locations, NA should be used for empty locations.

Returns

BatchContainer, invisibly

Method score()

Score current sample assignment,

Usage
BatchContainer$score(scoring)
Arguments
scoring

a function or a names list of scoring functions. Each function should return a numeric vector.

Returns

Returns a named vector of all scoring functions values.

Method copy()

Create an independent copy (clone) of a BatchContainer

Usage
BatchContainer$copy()
Returns

Returns a new BatchContainer

Method print()

Prints information about BatchContainer.

Usage
BatchContainer$print(...)
Arguments
...

not used.

Method scores_table()

Return a table with scores from an optimization.

Usage
BatchContainer$scores_table(index = NULL, include_aggregated = FALSE)
Arguments
index

optimization index, all by default

include_aggregated

include aggregated scores

Returns

a tibble::tibble() with scores

Method plot_trace()

Plot trace

Usage
BatchContainer$plot_trace(index = NULL, include_aggregated = FALSE, ...)
Arguments
index

optimization index, all by default

include_aggregated

include aggregated scores

...

not used.

Returns

a ggplot2::ggplot() object List of scoring functions. Tibble with batch container locations. Tibble with sample information and sample ids. Sample attributes, a data.table. Vector with assignment of sample ids to locations. Cached data.table with samples assignment. Validate sample assignment.

Examples


## ------------------------------------------------
## Method `BatchContainer$new`
## ------------------------------------------------

bc <- BatchContainer$new(
  dimensions = list(
    "plate" = 3,
    "row" = list(values = letters[1:3]),
    "column" = list(values = c(1, 3))
  ),
  exclude = data.frame(plate = 1, row = "a", column = c(1, 3), stringsAsFactors = FALSE)
)

bc
[Package designit version 0.5.0 Index]