R6 Class representing a batch container.
Describes container dimensions and samples to container location assignment.
A typical workflow starts with creating a BatchContainer. Then samples can be assigned to locations in that container.
## ------------------------------------------------ ## 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
trace: Optimization trace, a tibble::tibble()
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.
new()Create a new BatchContainer object.
BatchContainer$new(locations_table, dimensions, exclude = NULL)
locations_table: A table with available locations.
dimensions: A vector or list of dimensions. Every dimension should have a name. Could be an integer vector of dimensions or a named list. Every value of a list could be either dimension size or parameters for BatchContainerDimension$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.
bc <- BatchContainer$new(
dimensions = list(
"plate" = 3,
"row" = list(values = letters[1:3]),
"column" = list(values = c(1, 3))
),
exclude = data.frame(plate = 1, row = "a", column = c(1, 3), stringsAsFactors = FALSE)
)
bc
get_samples()Return table with samples and sample assignment.
BatchContainer$get_samples(
assignment = TRUE,
include_id = FALSE,
remove_empty_locations = FALSE,
as_tibble = TRUE
)
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.
table with samples and sample assignment.
get_locations()Get a table with all the locations in a BatchContainer.
BatchContainer$get_locations()
A tibble with all the available locations.
move_samples()Move samples between locations
This method can receive either src and dst or locations_assignment.
BatchContainer$move_samples(src, dst, location_assignment)
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.
BatchContainer, invisibly
score()Score current sample assignment,
BatchContainer$score(scoring)
scoring: a function or a names list of scoring functions. Each function should return a numeric vector.
Returns a named vector of all scoring functions values.
copy()Create an independent copy (clone) of a BatchContainer
BatchContainer$copy()
Returns a new BatchContainer
print()Prints information about BatchContainer.
BatchContainer$print(...)
...: not used.
scores_table()Return a table with scores from an optimization.
BatchContainer$scores_table(index = NULL, include_aggregated = FALSE)
index: optimization index, all by default
include_aggregated: include aggregated scores
a tibble::tibble() with scores
plot_trace()Plot trace
BatchContainer$plot_trace(index = NULL, include_aggregated = FALSE, ...)
index: optimization index, all by default
include_aggregated: include aggregated scores
...: not used.
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.
Useful links