Title:	A Computational Biologist’s Toolkit To Get Data From 'avidaDB'
Version:	1.2.1
Description:	Easy-to-use tools for performing complex queries on 'avidaDB', a semantic database that stores genomic and transcriptomic data of self-replicating computer programs (known as digital organisms) that mutate and evolve within a user-defined computational environment.
License:	MIT + file LICENSE
URL:	https://gitlab.com/fortunalab/avidaR
Encoding:	UTF-8
Language:	en-US
RoxygenNote:	7.3.1
Depends:	R (≥ 3.6.0)
Imports:	base64enc (≥ 0.1-3), xml2 (≥ 1.3.2), httr (≥ 1.4.2), dplyr (≥ 1.0.6), readr (≥ 1.4.0), tidyr (≥ 1.1.2), tibble (≥ 3.0.6), circlize (≥ 0.4.11), RColorBrewer, R6, curl (≥ 5.0.2)
Suggests:	testthat (≥ 3.0.0)
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2024-06-21 16:54:53 UTC; root
Author:	Miguel A. Fortuna [aut], Raúl Ortega [cre]
Maintainer:	Raúl Ortega <raul.ortega@ebd.csic.es>
Repository:	CRAN
Date/Publication:	2024-06-21 17:50:02 UTC

Converts a genome instruction sequence into a digital organism file

Description

Converts a digital organism instruction set into a digital genome instruction sequence.

Usage

convert_org_into_seq(
  org,
  inst_set = "heads",
  save = FALSE,
  file_name = NULL,
  save_path = getwd(),
  format = "seq",
  silent = FALSE
)

Arguments

Value

String of characters.

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

sequence <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[[1]]

convert_seq_into_org(genome_seq = sequence)

Converts a genome instruction sequence into a digital organism file

Description

Converts a genome instruction sequence into a digital organism file.

Usage

convert_seq_into_org(
  genome_seq,
  inst_set = "heads",
  save = FALSE,
  file_name = NULL,
  save_path = getwd(),
  format = "org",
  silent = FALSE
)

Arguments

Value

Data frame. Column names: "instruction".

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

sequence <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[[1]]

convert_seq_into_org(genome_seq = sequence)

Get database summary

Description

Get a summary of the data stored.

Usage

get_db_summary(triplestore)

Arguments

Value

Data frame: Columns: "data type", "value".

Examples

avidaDB <- triplestore_access$new()

avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

get_db_summary(triplestore = avidaDB)

Get docker image from experiment

Description

get the docker image built to run the experiment, which guarantees reproducibility .

Usage

get_docker_image_from_experiment_id(avida_experiment_id, triplestore)

Arguments

Value

Data frame. Columns: "avida_experiment_id" "docker_image_id" "id" "repo_digest"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single paper
get_docker_image_from_experiment_id(
  avida_experiment_id = 1,
  triplestore = avidaDB
)

# More than one experiment
get_docker_image_from_experiment_id(
  avida_experiment_id = c(1, 2, 3, 4),
  triplestore = avidaDB
)

Get doi from experiment

Description

Get the DOI of the scientific publication that documents the experiment carried out.

Usage

get_doi_from_experiment_id(avida_experiment_id, triplestore)

Arguments

Value

Data frame. Columns: "doi" "avida_experiment_id"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single paper
get_doi_from_experiment_id(
  avida_experiment_id = 1,
  triplestore = avidaDB
)

# More than one experiment
get_doi_from_experiment_id(
  avida_experiment_id = c(1, 2, 4),
  triplestore = avidaDB
)

Get experiment from organism

Description

Get the experiment identifier and description from which a digital organism is derived.

Usage

get_experiment_id_from_organism_id(
  organism_id,
  triplestore,
  description = FALSE
)

Arguments

Value

Data frame. Columns: "organism_id" "avida_experiment_id"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single organism
get_experiment_id_from_organism_id(organism_id = 1, triplestore = avidaDB)

# More than one organism
get_experiment_id_from_organism_id(
  organism_id = c(1, 2, 3),
  triplestore = avidaDB
)

Get genome from genome sequence

Description

Get the genome of a digital organism from the linear string of letters representing the instruction codes that make up its genome.

Usage

get_genome_id_from_genome_seq(genome_seq, triplestore)

Arguments

Value

Data frame. Columns: "genome_id" "genome_seq"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Get sequence for genome_1
sequence <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[1]

# Get genome id from sequence
get_genome_id_from_genome_seq(
  genome_seq = sequence,
  triplestore = avidaDB
)

Get genome from logic operations

Description

Get the genome of a digital organism that encodes a unique combination of logic operations for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_genome_id_from_logic_operation(
  logic_operation,
  seed_id = sample(1:1000, 1),
  genome_seq = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_id", "genome_seq" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single logic operation
get_genome_id_from_logic_operation(
  logic_operation = "not-or",
  triplestore = avidaDB
)

# More than one logic operation
get_genome_id_from_logic_operation(
  logic_operation = c("not", "not-and"),
  triplestore = avidaDB
)

# At seed_1
get_genome_id_from_logic_operation(
  logic_operation = c("or", "equals", "and"),
  seed_id = 1,
  genome_seq = TRUE,
  triplestore = avidaDB
)

Get genome from phenotype

Description

Get the genome of a digital organism that encodes a specific phenotype for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_genome_id_from_phenotype_id(
  phenotype_id,
  seed_id = sample(1:1000, 1),
  genome_seq = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "phenotype_id", "genome_seq" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single phenotype
get_genome_id_from_phenotype_id(phenotype_id = 1, triplestore = avidaDB)

# More than one phenotype
get_genome_id_from_phenotype_id(
  phenotype_id = c(1, 2),
  genome_seq = TRUE,
  triplestore = avidaDB
)

# At seeds_4 and seed_5
get_genome_id_from_phenotype_id(
  phenotype_id = c(1, 2),
  seed_id = c(4, 5),
  triplestore = avidaDB
)

Get genome from transcriptome

Description

Get the genome of a digital organism that executes a specific transcriptome for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_genome_id_from_transcriptome_id(
  transcriptome_id,
  seed_id = FALSE,
  genome_seq = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "genome_seq" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single transcriptome
get_genome_id_from_transcriptome_id(
  transcriptome_id = 1,
  triplestore = avidaDB
)

# More than one transcriptome
get_genome_id_from_transcriptome_id(
  transcriptome_id = c(1, 2, 3),
  genome_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_genome_id_from_transcriptome_id(
  transcriptome_id = 1,
  seed_id = c(1, 2),
  triplestore = avidaDB
)

Get genomes of wild-type organisms

Description

Get the genome of the digital organisms that were used as wild-type organisms to get their single-point mutants by calling the function get_mutant_at_pos.

Usage

get_genome_id_of_wild_type_organisms(triplestore)

Arguments

Value

Data frame: "genome_id_wild_type".

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

get_genome_id_of_wild_type_organisms(triplestore = avidaDB)

Get genome sequence from genome

Description

Get the linear string of letters representing the instruction codes that make up the genome of a digital organism from the id of the genome of a digital organism.

Usage

get_genome_seq_from_genome_id(genome_id, triplestore)

Arguments

Value

Data frame. Columns: "genome_id" "genome_seq"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single genome
get_genome_seq_from_genome_id(1, triplestore = avidaDB)

# More than one genome
get_genome_seq_from_genome_id(
  genome_id = c(1, 2, 3, 4),
  triplestore = avidaDB
)

Get the logic operations computed by a digital organism whose genome encodes a specific phenotype

Description

Get the logic operations encoded by a digital organism having the requested phenotype.

Usage

get_logic_operation_from_phenotype_id(
  phenotype_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "phenotype_id", "phenotype_binary" (optional), "equals", "exclusive-or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not"

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# One phenotype
get_logic_operation_from_phenotype_id(
  phenotype_id = 1,
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# More than one phenotype
get_logic_operation_from_phenotype_id(
  phenotype_id = c(1,2,3),
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# All phenotypes
get_logic_operation_from_phenotype_id(triplestore = avidaDB)

Get single-point mutants of wild-type organisms

Description

Get the genome sequence of a digital organism (i.e., wild-type) and its single-point mutants.

Usage

get_mutant_at_pos(
  genome_id = NULL,
  inst_replaced = NULL,
  inst_replaced_by = NULL,
  pos = NULL,
  triplestore
)

Arguments

Value

Data frame: Columns: "genome_id_wild_type", "genome_seq_wild_type", "genome_id_mutant", genome_seq_mutant", "pos".

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

get_mutant_at_pos(
  genome_id = 582,
  inst_replaced = 'o',
  inst_replaced_by = 'a',
  pos = 1,
  triplestore = avidaDB)

Get phenotype from genome

Description

Get the phenotype encoded by the genome of a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_phenotype_id_from_genome_id(
  genome_id,
  seed_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_id", "phenotype_id" "phenotype_binary" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single genome
get_phenotype_id_from_genome_id(genome_id = 1, triplestore = avidaDB)

# More than one genome at seed_1
get_phenotype_id_from_genome_id(
  genome_id = c(1, 2, 3),
  seed_id = 1,
  triplestore = avidaDB
)

# More than one genome at more than one seed (e.g., seed_3 and seed_4)
get_phenotype_id_from_genome_id(
  genome_id = 1,
  seed_id = c(3, 4),
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

Get phenotype from genome sequence

Description

Get the phenotype encoded by the instruction sequence constituting the genome of a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_phenotype_id_from_genome_seq(
  genome_seq,
  seed_id = FALSE,
  genome_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_id" (optional), "genome_seq", "phenotype_id", "phenotype_binary" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Get sequences for genomes_1 and genome_2
sequence1 <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[1]

sequence2 <- get_genome_seq_from_genome_id(
  genome_id = 2,
  triplestore = avidaDB
)$genome_seq[1]

# Single genome
get_phenotype_id_from_genome_seq(
  genome_seq = sequence1,
  triplestore = avidaDB
)

# More than one genome
get_phenotype_id_from_genome_seq(
  genome_seq = c(sequence1, sequence2),
  genome_id = TRUE,
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_phenotype_id_from_genome_seq(
  genome_seq = sequence2,
  seed_id = c(1, 2),
  triplestore = avidaDB
)

Get phenotype from logic operations

Description

Get the phenotype encoded by the genome of a digital organism that is specified by a unique combination of logic operations.

Usage

get_phenotype_id_from_logic_operation(
  logic_operation,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "phenotype_id", "phenotype_binary" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single logic operation
get_phenotype_id_from_logic_operation(
  logic_operation = "not-or",
  triplestore = avidaDB
)

# More than one logic operation
ops <- c("equals", "exclusive or", "not-or", "and-not", "or", "orn-not")

get_phenotype_id_from_logic_operation(
  logic_operation = ops,
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

Get phenotype from transcriptome

Description

Get the phenotype encoded by the genome of a digital organism that executes a specific transcriptome for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_phenotype_id_from_transcriptome_id(
  transcriptome_id,
  seed_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "phenotype_id", "phenotype_binary" (optional)

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single transcriptome
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = 53674,
  triplestore = avidaDB
)

# More than one transcriptome
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = c(53674, 1666099),
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_3
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = 53674, seed_id = c(1,3),
  triplestore = avidaDB
)

Get tandem repeat from genome

Description

Get the tandem repeat contained in the transcriptome of a digital organism having a specific genome.

Usage

get_tandem_id_from_genome_id(
  genome_id,
  seed_id = FALSE,
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single genome
get_tandem_id_from_genome_id(genome_id = 1, triplestore = avidaDB)

# More than one genome
get_tandem_id_from_genome_id(
  genome_id = c(1, 2, 3),
  tandem_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1, seed_3 and seed_5
get_tandem_id_from_genome_id(
  genome_id = 2,
  seed_id = c(1, 3, 5),
  tandem_pos = TRUE,
  triplestore = avidaDB
)

Get tandem repeat from genome sequence

Description

Get the tandem repeat contained in the transcriptome of a digital organism having a specific linear string of letters representing the instruction codes that make up its genome.

Usage

get_tandem_id_from_genome_seq(
  genome_seq,
  seed_id = FALSE,
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Column: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos (optional)."

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Get sequences for genomes 1 and 2
sequence1 <- get_genome_seq_from_genome_id(
  1,
  triplestore = avidaDB
)$genome_seq

sequence2 <- get_genome_seq_from_genome_id(
  2,
  triplestore = avidaDB
)$genome_seq

# Single genome
get_tandem_id_from_genome_seq(
  genome_seq = sequence1,
  triplestore = avidaDB
 )

# More than one genome
get_tandem_id_from_genome_seq(
  genome_seq = c(sequence1, sequence2),
  tandem_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_tandem_id_from_genome_seq(
  genome_seq = sequence2,
  seed_id = c(1,2),
  tandem_seq = TRUE,
  tandem_pos = TRUE,
  triplestore = avidaDB
)

Get tandem repeat from logic operations

Description

Get the tandem repeat contained in the transcriptome of a digital organism that executes a specific combination of logic operations.

Usage

get_tandem_id_from_logic_operation(
  logic_operation,
  seed_id = sample(1:1000, 1),
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "tandem_id", "tandem_seq" (optional), "tandem_pos" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single logic operation
get_tandem_id_from_logic_operation(
  logic_operation = "not",
  triplestore = avidaDB
)

# More than one logic operation
get_tandem_id_from_logic_operation(
  logic_operation = c("not", "and"),
  tandem_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_tandem_id_from_logic_operation(
  logic_operation = c("not", "and"),
  tandem_seq = TRUE,
  tandem_pos = TRUE,
  seed_id = c(1,2),
  triplestore = avidaDB
)

Get tandem repeat from phenotype

Description

Get the tandem repeat contained in the transcriptome of a digital organism that encodes a specific phenotype for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_tandem_id_from_phenotype_id(
  phenotype_id,
  seed_id = sample(1:1000, 1),
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Column: "seed_id" (optional), "phenotype_id", "tandem_id", "tandem_seq" (optional), "tandem_pos (optional)."

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single phenotype
get_tandem_id_from_phenotype_id(
  phenotype_id = 8, tandem_seq = TRUE,
  triplestore = avidaDB
)

# More than one phenotype at seed_1
get_tandem_id_from_phenotype_id(
  phenotype_id = c(2, 4, 8), seed_id = 1,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_tandem_id_from_phenotype_id(
  phenotype_id = 1,
  seed_id = c(1, 2),
  tandem_pos = TRUE,
  triplestore = avidaDB
)

Get the tandem repeat sequence from tandem repeat

Description

Get the tandem sequence from the tandem repeat contained in the transcriptome of a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_tandem_seq_from_tandem_id(
  tandem_id,
  seed_id = FALSE,
  genome_id = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "tandem_id", "tandem_seq", "tandem_pos" (optional), genome_id" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single tandem
get_tandem_seq_from_tandem_id(
  tandem_id = 6336945,
  triplestore = avidaDB
)

# More than one tandem at seed_1
get_tandem_seq_from_tandem_id(
  tandem_id = c(6336945, 2520963, 2520963),
  seed_id = 1,
  triplestore = avidaDB
)

# At seed_3 and seed_5
get_tandem_seq_from_tandem_id(
  tandem_id = 6336945,
  seed_id = c(1, 3),
  tandem_pos = TRUE,
  genome_id = TRUE,
  triplestore = avidaDB
)

Get transcriptome from genome

Description

Get the transcriptome of a digital organism having a specific genome for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_id_from_genome_id(
  genome_id,
  seed_id = FALSE,
  transcriptome_seq = FALSE,
  transcriptome_pos = FALSE,
  genome_seq = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_id", "genome_seq" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Singel genome
get_transcriptome_id_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)

# More than one genome
get_transcriptome_id_from_genome_id(
  genome_id = c(1, 2),
  transcriptome_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_3
get_transcriptome_id_from_genome_id(
  genome_id = 2,
  seed_id = c(1, 3),
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)

Get transcriptome from genome sequence

Description

Get the transcriptome of a digital organism having a specific linear string of letters representing the instruction codes that make up its genome for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_id_from_genome_seq(
  genome_seq,
  seed_id = FALSE,
  transcriptome_seq = FALSE,
  transcriptome_pos = FALSE,
  genome_id = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "genome_seq", "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Get sequences for genome_1 and genome_2
sequence1 <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[1]

sequence2 <- get_genome_seq_from_genome_id(
  genome_id = 2,
  triplestore = avidaDB
)$genome_seq[1]

# Single genome
get_transcriptome_id_from_genome_seq(
  genome_seq = sequence1,
  triplestore = avidaDB
)

# More than one genome
get_transcriptome_id_from_genome_seq(
  genome_seq = c(sequence1, sequence2),
  transcriptome_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_transcriptome_id_from_genome_seq(
  genome_seq = sequence2,
  seed_id = c(1,2),
  transcriptome_seq = TRUE,
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)

Get transcriptome from logic operations

Description

Get the transcriptome of a digital organism that executes a specific combination of logic operations for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_id_from_logic_operation(
  logic_operation,
  seed_id = sample(1:1000, 1),
  transcriptome_seq = FALSE,
  transcriptome_pos = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional)

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single logic operation
get_transcriptome_id_from_logic_operation(
  logic_operation = "not",
  triplestore = avidaDB
)

# More than one logic operation
get_transcriptome_id_from_logic_operation(
  logic_operation = c("not", "and"),
  transcriptome_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_transcriptome_id_from_logic_operation(
  logic_operation = c("not", "and"),
  seed_id = c(1,2),
  transcriptome_seq = TRUE,
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)

Get transcriptome from phenotype

Description

Get the transcriptome of a digital organism whose genome encodes a specific phenotype for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_id_from_phenotype_id(
  phenotype_id,
  seed_id = sample(1:1000, 1),
  transcriptome_seq = FALSE,
  transcriptome_pos = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional), "phenotype_id", "phenotype_binary" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single phenotype
get_transcriptome_id_from_phenotype_id(
  phenotype_id = 1,
  transcriptome_seq = TRUE,
  triplestore = avidaDB
)

# More than one phenotype at seed_1
get_transcriptome_id_from_phenotype_id(
  phenotype_id = c(1, 2), seed_id = 1,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_transcriptome_id_from_phenotype_id(
  phenotype_id = 1,
  seed_id = c(1, 2),
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)

Get transcriptome sequence from transcriptome

Description

Get the transcriptome sequence of the transcriptome executed by a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id,
  seed_id = FALSE,
  transcriptome_pos = FALSE,
  genome_seq = FALSE,
  triplestore
)

Arguments

Value

data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq", "transcriptome_pos" (optional), "genome_seq" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single transcriptome
get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = 53674,
  triplestore = avidaDB
)

# More than one transcriptome at seed_1
get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = c(53674, 1666099),
  seed_id = 1,
  triplestore = avidaDB
)

# At seed_1 and seed_3
get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = 2,
  seed_id = c(1, 3),
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)

Get the genetic language of Avida

Description

List of the instruction codes comprising the genetic language of digital organisms in Avida.

Usage

instruction_set(inst_set = "heads")

Arguments

Value

Data frame. Columns: "instruction", "letter", "color"

Get the list of logic operations that a digital organism can compute

Description

List of the logic operations that a digital organism can execute.

Usage

logic_operation()

Value

Vector of character.

Get a plot of the transcriptome as a chord diagram

Description

Get a plot of the transcriptome executed by a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

plot_transcriptome(
  transcriptome_id,
  seed_id = NULL,
  inst_set = "heads",
  save = FALSE,
  file_name = NULL,
  save_path = "~/transcriptome@chords",
  format = "svg",
  silent = FALSE,
  triplestore
)

Arguments

Examples

# Create triplestore object
triplestore <- triplestore_access$new()

# Set access options
triplestore$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# plot transcriptome 53674 at seed_1 and save to disk in pdf format
plot_transcriptome(
  transcriptome_id = 53674,
  seed_id = 1,
  save = FALSE,
  save_path = getwd(),
  format = "pdf",
  triplestore = triplestore
)

Class to manage triplestore access options

Description

Class to manage triplestore access options

Methods

Public methods

• triplestore_access$new()

• triplestore_access$get_access_options()

• triplestore_access$set_access_options()

• triplestore_access$submit_query()

• triplestore_access$ontology()

• triplestore_access$clone()

Method new()

Create and initialize the object.

Usage

triplestore_access$new()

Returns

Object of class triplestore_access.

Method get_access_options()

Get access options

Usage

triplestore_access$get_access_options()

Returns

list containing URL of the API server, user credentials, repository name, authentication status, and SPARQL protocol version

Method set_access_options()

Set authentication access options for graphdb triplestore

Usage

triplestore_access$set_access_options(
  url = NULL,
  user = NULL,
  password = NULL,
  repository = NULL,
  timeout = 100
)

Arguments

Method submit_query()

Submit a SPARQL query to the triplestore to obtain data

Usage

triplestore_access$submit_query(query)

Arguments

Method ontology()

Show ontology information

Usage

triplestore_access$ontology()

Returns

List containing title, description and versionIRI of the ontology

Method clone()

The objects of this class are cloneable with this method.

Usage

triplestore_access$clone(deep = FALSE)

Arguments

Examples

# Create object triplestore

triplestore <- triplestore_access$new()


# Set options to access a specific triple-store implemented in GraphDB

triplestore$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)


# Show current access options

triplestore$get_access_options()


# Querying data with SPARQL

triplestore$submit_query('PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
                          PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
                          select ?tandem_id where { 
                            ?digital_tandem_repeat rdfs:label "digital tandem repeat"@en .
                            ?tandem_id a ?digital_tandem_repeat .
                          } limit 10')


# Show ontology info

triplestore$ontology()