, Raúl Ortega [cre]
| Title: | A Computational Biologist’s Toolkit To Get Data From 'avidaDB' |
|---|---|
| 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. |
| Authors: | Miguel A. Fortuna [aut]
, Raúl Ortega [cre]
|
| Maintainer: | Raúl Ortega <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.2.1 |
| Built: | 2024-12-21 06:49:47 UTC |
| Source: | CRAN |
Converts a digital organism instruction set into a digital genome instruction sequence.
convert_org_into_seq( org, inst_set = "heads", save = FALSE, file_name = NULL, save_path = getwd(), format = "seq", silent = FALSE )convert_org_into_seq( org, inst_set = "heads", save = FALSE, file_name = NULL, save_path = getwd(), format = "seq", silent = FALSE )
org |
Data Frame. Column names: |
inst_set |
Name of the instruction set. It must be one of the
following: |
save |
Logical value (TRUE/FALSE) indicating whether the output should or should not be saved to a file ("FALSE" by default). |
file_name |
String of characters representing the name of the file without any extension ("genome.seq" by default). |
save_path |
String of characters representing the name of the folder where the digital organism file will be saved. |
format |
String of characters representing the format of the file ("seq" by default). |
silent |
Logical value (TRUE/FALSE) to show/hide messages ("FALSE" by default). |
String of characters.
# 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 )$genome_seq[[1]] convert_seq_into_org(genome_seq = sequence)# Create triplestore object avidaDB <- triplestore_access$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.
convert_seq_into_org( genome_seq, inst_set = "heads", save = FALSE, file_name = NULL, save_path = getwd(), format = "org", silent = FALSE )convert_seq_into_org( genome_seq, inst_set = "heads", save = FALSE, file_name = NULL, save_path = getwd(), format = "org", silent = FALSE )
genome_seq |
String of letters. |
inst_set |
Name of the instruction set. It must be one of the
following: |
save |
Logical value (TRUE/FALSE) indicating whether the output should or should not be saved to a file ("FALSE" by default). |
file_name |
String of characters representing the name of the file without any extension ("organism.org" by default). |
save_path |
String of characters representing the name of the folder where the digital organism file will be saved. |
format |
String of characters representing the format of the file ("org" by default). |
silent |
Logical value (TRUE/FALSE) to show/hide messages ("FALSE" by default). |
Data frame. Column names: "instruction".
# 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 )$genome_seq[[1]] convert_seq_into_org(genome_seq = sequence)# Create triplestore object avidaDB <- triplestore_access$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 a summary of the data stored.
get_db_summary(triplestore)get_db_summary(triplestore)
triplestore |
Object of class triplestore_access which manages database access. |
Data frame: Columns: "data type", "value".
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)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 the docker image built to run the experiment, which guarantees reproducibility .
get_docker_image_from_experiment_id(avida_experiment_id, triplestore)get_docker_image_from_experiment_id(avida_experiment_id, triplestore)
avida_experiment_id |
Integer or a vector of integer values. |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "avida_experiment_id" "docker_image_id" "id" "repo_digest"
# 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 )# 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 the DOI of the scientific publication that documents the experiment carried out.
get_doi_from_experiment_id(avida_experiment_id, triplestore)get_doi_from_experiment_id(avida_experiment_id, triplestore)
avida_experiment_id |
Integer or a list of integer values. |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "doi" "avida_experiment_id"
# 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 )# 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 the experiment identifier and description from which a digital organism is derived.
get_experiment_id_from_organism_id( organism_id, triplestore, description = FALSE )get_experiment_id_from_organism_id( organism_id, triplestore, description = FALSE )
organism_id |
Integer or a list of integer values. |
triplestore |
Object of class triplestore_access which manages database access. |
description |
Logical value (TRUE/FALSE) to show/hide the description of the experiment (FALSE by default). |
Data frame. Columns: "organism_id" "avida_experiment_id"
# 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 )# 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 the genome of a digital organism from the linear string of letters representing the instruction codes that make up its genome.
get_genome_id_from_genome_seq(genome_seq, triplestore)get_genome_id_from_genome_seq(genome_seq, triplestore)
genome_seq |
String of letters or a list of strings |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "genome_id" "genome_seq"
# 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 )$genome_seq[1] # Get genome id from sequence get_genome_id_from_genome_seq( genome_seq = sequence, triplestore = avidaDB )# Create triplestore object avidaDB <- triplestore_access$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 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).
get_genome_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), genome_seq = FALSE, triplestore )get_genome_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), genome_seq = FALSE, triplestore )
logic_operation |
List of logical operations from the following set: "equals", "exclusive-or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not". |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
genome_seq |
Logical value (TRUE/FALSE) to show/hide this column ("FALSE" by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_id", "genome_seq" (optional).
# 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 )# 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 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).
get_genome_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), genome_seq = FALSE, triplestore )get_genome_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), genome_seq = FALSE, triplestore )
phenotype_id |
Integer or a list of integer values. |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
genome_seq |
Logical value (TRUE/FALSE) to show/hide this column ("FALSE" by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "phenotype_id", "genome_seq" (optional).
# 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 )# 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 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).
get_genome_id_from_transcriptome_id( transcriptome_id, seed_id = FALSE, genome_seq = FALSE, triplestore )get_genome_id_from_transcriptome_id( transcriptome_id, seed_id = FALSE, genome_seq = FALSE, triplestore )
transcriptome_id |
Integer or a list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
genome_seq |
Logical value (TRUE/FALSE) to show/hide this column ("FALSE" by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "transcriptome_id", "genome_seq" (optional).
# 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 )# 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 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.
get_genome_id_of_wild_type_organisms(triplestore)get_genome_id_of_wild_type_organisms(triplestore)
triplestore |
Object of class triplestore_access which manages database access. |
Data frame: "genome_id_wild_type".
# 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)# 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 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.
get_genome_seq_from_genome_id(genome_id, triplestore)get_genome_seq_from_genome_id(genome_id, triplestore)
genome_id |
Integer or a list of integer values. |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "genome_id" "genome_seq"
# 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 )# 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 encoded by a digital organism having the requested phenotype.
get_logic_operation_from_phenotype_id( phenotype_id = FALSE, phenotype_binary = FALSE, triplestore )get_logic_operation_from_phenotype_id( phenotype_id = FALSE, phenotype_binary = FALSE, triplestore )
phenotype_id |
Integer, a vector of integers (from 0 to 511), or a logical value (if FALSE, the function returns the entire phenotype space). |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide phenotype_id in binary notation (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "phenotype_id", "phenotype_binary" (optional), "equals", "exclusive-or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not"
# 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)# 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 the genome sequence of a digital organism (i.e., wild-type) and its single-point mutants.
get_mutant_at_pos( genome_id = NULL, inst_replaced = NULL, inst_replaced_by = NULL, pos = NULL, triplestore )get_mutant_at_pos( genome_id = NULL, inst_replaced = NULL, inst_replaced_by = NULL, pos = NULL, triplestore )
genome_id |
Integer or a list of integer values. If not specified, the function will return the single-point mutants of a randomly chosen wild-type organism. |
inst_replaced |
A letter representing the instruction of the genome sequence of the wild-type organism to be mutated. If not specified, the function will return the single-point mutants that have replaced the letter that the genome of the wild-type organism carried at that position (if the position is specified, otherwise it will return the mutations located on all positions) by the letter indicated in the argument inst_replaced_by (if specified, otherwise it will return all the mutants at that position on the genome of the wild type organism). |
inst_replaced_by |
A letter representing the instruction of the genome of the single-point mutant that have replaced the instruction of the genome of the wild-type organism. If not specified, the function will return all single-point mutants that have replaced the letter indicated in the argument inst_replaced (if specified, otherwise it will return all the mutants at that position on the genome of the wild type organism) of the genome of the wild-type organism at that position (if the position is specified, otherwise it will return the mutations located on all positions). |
pos |
Integer representing the position of the single-point mutation along the genome of a digital organism (from 1 to 100 for a genome length of 100 instructions). If not specified, the function will return all single-point mutants of the genome of the wild-type organism. |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame: Columns: "genome_id_wild_type", "genome_seq_wild_type", "genome_id_mutant", genome_seq_mutant", "pos".
# 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)# 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 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).
get_phenotype_id_from_genome_id( genome_id, seed_id = FALSE, phenotype_binary = FALSE, triplestore )get_phenotype_id_from_genome_id( genome_id, seed_id = FALSE, phenotype_binary = FALSE, triplestore )
genome_id |
Integer or a list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide phenotype_id in binary notation (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_id", "phenotype_id" "phenotype_binary" (optional).
# 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 )# 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 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).
get_phenotype_id_from_genome_seq( genome_seq, seed_id = FALSE, genome_id = FALSE, phenotype_binary = FALSE, triplestore )get_phenotype_id_from_genome_seq( genome_seq, seed_id = FALSE, genome_id = FALSE, phenotype_binary = FALSE, triplestore )
genome_seq |
String of letters or a list of strings. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
genome_id |
Logical value (TRUE/FALSE) to show/hide genome_id (FALSE by default). |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide phenotype_id in binary notation (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_id" (optional), "genome_seq", "phenotype_id", "phenotype_binary" (optional).
# 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 )# 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 the phenotype encoded by the genome of a digital organism that is specified by a unique combination of logic operations.
get_phenotype_id_from_logic_operation( logic_operation, phenotype_binary = FALSE, triplestore )get_phenotype_id_from_logic_operation( logic_operation, phenotype_binary = FALSE, triplestore )
logic_operation |
List of logical functions from the following set: "equals", "exclusive-or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not". |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide the phenotype in binary notation (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "phenotype_id", "phenotype_binary" (optional).
# 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 )# 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 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).
get_phenotype_id_from_transcriptome_id( transcriptome_id, seed_id = FALSE, phenotype_binary = FALSE, triplestore )get_phenotype_id_from_transcriptome_id( transcriptome_id, seed_id = FALSE, phenotype_binary = FALSE, triplestore )
transcriptome_id |
Integer or list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide phenotype in binary notation (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "transcriptome_id", "phenotype_id", "phenotype_binary" (optional)
# 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 )# 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 the tandem repeat contained in the transcriptome of a digital organism having a specific genome.
get_tandem_id_from_genome_id( genome_id, seed_id = FALSE, tandem_seq = FALSE, tandem_pos = FALSE, triplestore )get_tandem_id_from_genome_id( genome_id, seed_id = FALSE, tandem_seq = FALSE, tandem_pos = FALSE, triplestore )
genome_id |
Integer or a list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
tandem_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
tandem_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos" (optional).
# 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 )# 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 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.
get_tandem_id_from_genome_seq( genome_seq, seed_id = FALSE, tandem_seq = FALSE, tandem_pos = FALSE, triplestore )get_tandem_id_from_genome_seq( genome_seq, seed_id = FALSE, tandem_seq = FALSE, tandem_pos = FALSE, triplestore )
genome_seq |
String of letters or a list of strings. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
tandem_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
tandem_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Column: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos (optional)."
# 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 )# 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 the tandem repeat contained in the transcriptome of a digital organism that executes a specific combination of logic operations.
get_tandem_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), tandem_seq = FALSE, tandem_pos = FALSE, triplestore )get_tandem_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), tandem_seq = FALSE, tandem_pos = FALSE, triplestore )
logic_operation |
List of logical functions from the following set: "equals", "exclusive or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not". |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
tandem_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
tandem_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "tandem_id", "tandem_seq" (optional), "tandem_pos" (optional).
# 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 )# 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 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).
get_tandem_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), tandem_seq = FALSE, tandem_pos = FALSE, triplestore )get_tandem_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), tandem_seq = FALSE, tandem_pos = FALSE, triplestore )
phenotype_id |
Integer or list of integer values. |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
tandem_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
tandem_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Column: "seed_id" (optional), "phenotype_id", "tandem_id", "tandem_seq" (optional), "tandem_pos (optional)."
# 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 )# 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 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).
get_tandem_seq_from_tandem_id( tandem_id, seed_id = FALSE, genome_id = FALSE, tandem_pos = FALSE, triplestore )get_tandem_seq_from_tandem_id( tandem_id, seed_id = FALSE, genome_id = FALSE, tandem_pos = FALSE, triplestore )
tandem_id |
Integer or a list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
genome_id |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
tandem_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "tandem_id", "tandem_seq", "tandem_pos" (optional), genome_id" (optional).
# 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 )# 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 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).
get_transcriptome_id_from_genome_id( genome_id, seed_id = FALSE, transcriptome_seq = FALSE, transcriptome_pos = FALSE, genome_seq = FALSE, triplestore )get_transcriptome_id_from_genome_id( genome_id, seed_id = FALSE, transcriptome_seq = FALSE, transcriptome_pos = FALSE, genome_seq = FALSE, triplestore )
genome_id |
Integer or list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
transcriptome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
transcriptome_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
genome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_id", "genome_seq" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional).
# 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 )# 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 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).
get_transcriptome_id_from_genome_seq( genome_seq, seed_id = FALSE, transcriptome_seq = FALSE, transcriptome_pos = FALSE, genome_id = FALSE, triplestore )get_transcriptome_id_from_genome_seq( genome_seq, seed_id = FALSE, transcriptome_seq = FALSE, transcriptome_pos = FALSE, genome_id = FALSE, triplestore )
genome_seq |
String of letters or a list of strings. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
transcriptome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
transcriptome_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
genome_id |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "genome_seq", "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional).
# 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 )# 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 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).
get_transcriptome_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), transcriptome_seq = FALSE, transcriptome_pos = FALSE, triplestore )get_transcriptome_id_from_logic_operation( logic_operation, seed_id = sample(1:1000, 1), transcriptome_seq = FALSE, transcriptome_pos = FALSE, triplestore )
logic_operation |
List of logical functions from the following set: "equals", "exclusive or", "not-or", "and-not", "or", "orn-not", "and", "not-and", "not". |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
transcriptome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
transcriptome_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional)
# 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 )# 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 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).
get_transcriptome_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), transcriptome_seq = FALSE, transcriptome_pos = FALSE, phenotype_binary = FALSE, triplestore )get_transcriptome_id_from_phenotype_id( phenotype_id, seed_id = sample(1:1000, 1), transcriptome_seq = FALSE, transcriptome_pos = FALSE, phenotype_binary = FALSE, triplestore )
phenotype_id |
Integer or list of integer values. |
seed_id |
Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000). |
transcriptome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
transcriptome_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
phenotype_binary |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
Data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq" (optional), "transcriptome_pos" (optional), "phenotype_id", "phenotype_binary" (optional).
# 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 )# 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 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).
get_transcriptome_seq_from_transcriptome_id( transcriptome_id, seed_id = FALSE, transcriptome_pos = FALSE, genome_seq = FALSE, triplestore )get_transcriptome_seq_from_transcriptome_id( transcriptome_id, seed_id = FALSE, transcriptome_pos = FALSE, genome_seq = FALSE, triplestore )
transcriptome_id |
Integer or list of integer values. |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
transcriptome_pos |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
genome_seq |
Logical value (TRUE/FALSE) to show/hide this column (FALSE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
data frame. Columns: "seed_id" (optional), "transcriptome_id", "transcriptome_seq", "transcriptome_pos" (optional), "genome_seq" (optional).
# 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 )# 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 )
List of the instruction codes comprising the genetic language of digital organisms in Avida.
instruction_set(inst_set = "heads")instruction_set(inst_set = "heads")
inst_set |
Name of the instruction set. It must be one of the
following: "heads" (default), "heads-sex", or |
Data frame. Columns: "instruction", "letter", "color"
List of the logic operations that a digital organism can execute.
logic_operation()logic_operation()
Vector of character.
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).
plot_transcriptome( transcriptome_id, seed_id = NULL, inst_set = "heads", save = FALSE, file_name = NULL, save_path = "~/transcriptome@chords", format = "svg", silent = FALSE, triplestore )plot_transcriptome( transcriptome_id, seed_id = NULL, inst_set = "heads", save = FALSE, file_name = NULL, save_path = "~/transcriptome@chords", format = "svg", silent = FALSE, triplestore )
transcriptome_id |
Integer |
seed_id |
Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed. |
inst_set |
Name of the instruction set. It must be one of the
following: |
save |
Logical value (TRUE/FALSE) to save the plot (FALSE by default). |
file_name |
String of characters indicating the name of the file to be saved (without extension). |
save_path |
String of characters indicating the name of the folder where the file will be saved. |
format |
String of characters indicating the format of the file ("pdf" and "svg" are currently supported). |
silent |
Logical value (TRUE/FALSE) to show/hide messages (TRUE by default). |
triplestore |
Object of class triplestore_access which manages database access. |
# 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 )# 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
new()
Create and initialize the object.
triplestore_access$new()
Object of class triplestore_access.
get_access_options()
Get access options
triplestore_access$get_access_options()
list containing URL of the API server, user credentials, repository name, authentication status, and SPARQL protocol version
set_access_options()
Set authentication access options for graphdb triplestore
triplestore_access$set_access_options( url = NULL, user = NULL, password = NULL, repository = NULL, timeout = 100 )
urlString containing the URL of the triplestore server
userString containing the username if authentication is needed
passwordString containing the password if authentication is needed
repositoryString containing the ID of the repository to which you want to connect to
timeoutConnection timeout limit in seconds used for queries
submit_query()
Submit a SPARQL query to the triplestore to obtain data
triplestore_access$submit_query(query)
queryString containing the SPARQL query to retrieve data
ontology()
Show ontology information
triplestore_access$ontology()
List containing title, description and versionIRI of the ontology
clone()
The objects of this class are cloneable with this method.
triplestore_access$clone(deep = FALSE)
deepWhether to make a deep clone.
# 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$ontology()# Create object triplestore triplestore <- triplestore_access$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()