plot_transcriptome {avidaR}

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

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: heads (default), heads-sex, or transsmt. The names correspond to the instruction set configuration files (e.g., instset-heads.cfg for heads).

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.

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
)