Package 'biodbKegg'

Title: biodbKegg, a library for connecting to the KEGG Database
Description: The biodbKegg library is an extension of the biodb framework package that provides access to the KEGG databases Compound, Enzyme, Genes, Module, Orthology and Reaction. It allows to retrieve entries by their accession numbers. Web services like "find", "list" and "findExactMass" are also available. Some functions for navigating along the pathways have also been implemented.
Authors: Pierrick Roger [aut, cre]
Maintainer: Pierrick Roger <[email protected]>
License: AGPL-3
Version: 1.11.0
Built: 2024-07-13 05:21:35 UTC
Source: https://github.com/bioc/biodbKegg

Help Index

A class for representing a circle.

Description

A class for representing a circle.

A class for representing a circle.

Details

This class represents a rectangle, used for graphical representation. It is used by KeggPathwayConn::extractPathwayMapShapes() method.

Arguments to the constructor are:

x: X coordinate of center.

y: Y coordinate of center.

r: Radius.

Super class

biodbKegg::KeggShape -> KeggCircle

Methods

Public methods

Inherited methods

Method new()

Initialize new instance.

Usage
KeggCircle$new(x, y, r, ...)
Arguments
x

Abscissa of the circle's center.

y

Ordinate of the circle's center.

r

Radius of the circle.

...

Additional parameters are passed to super class' initializer.

Returns

Nothing.

Method getX()

Get the X coordinate.

Usage
KeggCircle$getX()
Returns

The X coordinate.

Method getY()

Get the Y coordinate.

Usage
KeggCircle$getY()
Returns

The Y coordinate.

Method getRadius()

Get the radius.

Usage
KeggCircle$getRadius()
Returns

The radius.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggCircle$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggShape, KeggRect.

Examples

# Create an instance
c1 <- KeggCircle$new(x=12, y=5, r=3)

# Since it inherits from KeggShape, a color and a label can be set
c2 <- KeggCircle$new(x=12, y=5, r=3, color='blue', label='Circle 2')

# Getting center
c1$getX()
c1$getY()

# Getting radius
c1#getRadius()

# Draw a circle on the current image

c1$draw()

The connector class to KEGG Compound database.

Description

The connector class to KEGG Compound database.

The connector class to KEGG Compound database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggCompoundConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggCompoundConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method wsFindExactMass()

Searches for entries by mass. You must either provide a single mass through 'mass' parameter or provide a range through 'mass.min' and 'mass.max'.

Usage
KeggCompoundConn$wsFindExactMass(
  mass = NULL,
  mass.min = NULL,
  mass.max = NULL,
  ...
)
Arguments
mass

Single mass.

mass.min

Minimal mass.

mass.max

Maximal mass.

...

parameters passed to KeggConn::wsFind().

See

http //www.kegg.jp/kegg/docs/keggapi.html for details.

Returns

wsFind().

Method wsFindMolecularWeight()

Searches for entries by molecular mass. You must either provide a single mass through 'mass' parameter or provide a range through 'mass.min' and 'mass.max'. See http //www.kegg.jp/kegg/docs/keggapi.html for details.

Usage
KeggCompoundConn$wsFindMolecularWeight(
  mass = NULL,
  mass.min = NULL,
  mass.max = NULL,
  ...
)
Arguments
mass

Single mass.

mass.min

Minimal mass.

mass.max

Maximal mass.

...

Parameters passed to KeggConn::wsFind().

Returns

wsFind().

Method getPathwayIdsPerCompound()

Gets organism pathways for each compound. This method retrieves for each compound the KEGG pathways of the organism in which the compound is involved.

Usage
KeggCompoundConn$getPathwayIdsPerCompound(id, org, limit = 3)
Arguments
id

A character vector of KEGG Compound IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

limit

The maximum number of modules IDs to retrieve for each compound. Set to 0 to disable.

Returns

A named list of KEGG pathway ID vectors, where the names of the list are the compound IDs."

Method getModuleIdsPerCompound()

Gets organism modules for each compound. This method retrieves for each compound the KEGG modules of the organism in which the compound is involved.

Usage
KeggCompoundConn$getModuleIdsPerCompound(id, org, limit = 3)
Arguments
id

A character vector of KEGG Compound IDs.

org

The organism in which to search for modules, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

limit

The maximum number of modules IDs to retrieve for each compound. Set to 0 to disable.

Returns

A named list of KEGG module ID vectors, where the names of the list are the compound IDs."

Method getPathwayIds()

Gets organism pathways. This method retrieves KEGG pathways of the specified organism in which the compounds are involved.

Usage
KeggCompoundConn$getPathwayIds(id, org)
Arguments
id

A character vector of KEGG Compound IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

Returns

A vector of KEGG pathway IDs.

Method addInfo()

Add informations (as new column appended to the end) to an existing data frame containing a column of KEGG Compound IDs.

Usage
KeggCompoundConn$addInfo(x, id.col, org, limit = 3, prefix = "")
Arguments
x

A data frame containing at least one column with Biodb entry IDs identified by the parameter 'id.col'.

id.col

The name of the column containing IDs inside the input data frame.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

limit

This is the maximum number of values obtained for each ID, for every column added, in case multiple values are obtained. Set to 0 to get all values.

prefix

Insert a prefix at the start of name of all new columns.

Returns

A data frame containing 'x' and new columns appended with KEGG identifiers and data.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggCompoundConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn, KeggPathwayConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector to KEGG Compound
conn <- mybiodb$getFactory()$createConn('kegg.compound')

# Search for compounds by exact mass
conn$wsFindExactMass(mass=174.05, retfmt='parsed')

# Search for compounds by molecular weight 
conn$wsFindMolecularWeight(mass=300, retfmt='parsed')

# Get pathway IDs related to compounds
pathway.ids=conn$getPathwayIds(c('C02648', 'C06144'), org='mmu')

# Terminate instance.
mybiodb$terminate()

KEGG Compound entry class.

Description

This is the entry class for the KEGG Compound database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggCompoundEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggCompoundEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.compound')

# Get an entry
e <- conn$getEntry('C00133')

# Terminate instance.
mybiodb$terminate()

The connector abstract class to KEGG databases.

Description

The connector abstract class to KEGG databases.

The connector abstract class to KEGG databases.

Details

This is the mother class of all KEGG connectors. It defines code common to all KEGG connectors.

The constructor accepts the following arguments:

db.name: The database name as defined in http://www.kegg.jp/kegg/docs/keggapi.html.

db.abbrev: The database abbreviated name, as defined in http://www.kegg.jp/kegg/docs/keggapi.html.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> KeggConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class. The parameters of this function are for the use of subclasses.

Usage
KeggConn$new(
  db.name = NA_character_,
  db.abbrev = NA_character_,
  accession.prefix = NA_character_,
  ...
)
Arguments
db.name

The database name as defined in www.kegg.jp/kegg/docs/keggapi.html.

db.abbrev

The database abbreviation as defined in www.kegg.jp/kegg/docs/keggapi.html.

accession.prefix

The prefix used for accession identifiers.

...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method wsList()

Gets the full list of entry IDs. See

Usage
KeggConn$wsList(retfmt = c("plain", "request", "ids"))
Arguments
retfmt

Use to set the format of the returned value. 'plain' will return the raw result from the server, as a character value. 'request' will return the request as it would have been sent, as a BiodbRequest object. 'ids' will return a character vector containing entry IDs.

http

//www.kegg.jp/kegg/docs/keggapi.html for details.

Returns

Depending on 'retfmt'.

Method wsFind()

Searches for entries. See http://www.kegg.jp/kegg/docs/keggapi.html for details.

Usage
KeggConn$wsFind(
  query,
  option = c("NONE", "formula", "exact_mass", "mol_weight", "nop"),
  retfmt = c("plain", "request", "parsed", "ids", "ids.no.prefix")
)
Arguments
query

The query to send to the database web service. When searching by mass (i.e. 'option' parameter set to either 'exact_mass' or 'mol_weight'), this query field must be set to either an exact (i.e. 174.05) or a range (i.e. '250-260').

option

Set this parameter to 'NONE' for querying on fields 'ENTRY', 'NAME', 'DESCRIPTION', 'COMPOSITION', 'DEFINITION' and 'ORTHOLOGY'. See http //www.kegg.jp/kegg/docs/keggapi.html for an exact list of fields that are searched for each database, and also for other possible values of this 'option' paramater.

retfmt

Use to set the format of the returned value. 'plain' will return the raw result from the server, as a character value. 'request' will return the request as it would have been sent, as a BiodbRequest object. 'parsed' will return a data frame. 'ids' will return a character vector containing the IDs of the matching entries.

Returns

Depending on 'retfmt'.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector to a KEGG database
conn <- mybiodb$getFactory()$createConn('kegg.compound')

# Search for an entry
conn$wsFind('NADPH', retfmt='parsed')

# Terminate instance.
mybiodb$terminate()

KEGG entry abstract class.

Description

This is the abstract entry class for all KEGG entry classes.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> KeggEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.compound')

# Get an entry
e <- conn$getEntry('C00133')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Enzyme database.

Description

The connector class to KEGG Enzyme database.

The connector class to KEGG Enzyme database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggEnzymeConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggEnzymeConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method getPathwayIds()

Gets organism pathways. This method retrieves KEGG pathways of the specified organism in which the enzymes are involved.

Usage
KeggEnzymeConn$getPathwayIds(id, org)
Arguments
id

A character vector of KEGG Compound IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

Returns

A vector of KEGG pathway IDs.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggEnzymeConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get connector
conn <- mybiodb$getFactory()$createConn('kegg.enzyme')

# Get pathway IDs related to enzymes
pathway.ids=conn$getPathwayIds(c('1.2.1.3', '3.7.1.3'), org='mmu')

# Terminate instance.
mybiodb$terminate()

KEGG Enzyme entry class.

Description

This is the entry class for the KEGG Enzyme class.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggEnzymeEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggEnzymeEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.enzyme')

# Get an entry
e <- conn$getEntry('1.1.1.54')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Pathway database.

Description

The connector class to KEGG Pathway database.

The connector class to KEGG Pathway database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggGenesConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggGenesConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method getPathwayIdsPerGene()

Gets organism pathways for each gene. This method retrieves for each gene the KEGG pathways of the organism in which the gene is involved.

Usage
KeggGenesConn$getPathwayIdsPerGene(id, org, limit = 3)
Arguments
id

A character vector of KEGG Gene IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

limit

The maximum number of modules IDs to retrieve for each gene. Set to 0 to disable.

Returns

A named list of KEGG pathway ID vectors, where the names of the list are the gene IDs."

Method getPathwayIds()

Gets organism pathways. This method retrieves KEGG pathways of the specified organism in which the genes are involved.

Usage
KeggGenesConn$getPathwayIds(id, org)
Arguments
id

A character vector of KEGG Genes IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

Returns

A vector of KEGG pathway IDs.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggGenesConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.genes')

# Get an entry
e <- conn$getEntry('mmu:14635')

# Terminate instance.
mybiodb$terminate()

KEGG Genes entry class.

Description

This is the entry class for the KEGG Genes database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggGenesEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggGenesEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.genes')

# Get an entry
e <- conn$getEntry('mmu:14635')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Glycan database.

Description

The connector class to KEGG Glycan database.

The connector class to KEGG Glycan database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggGlycanConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggGlycanConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggGlycanConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector to KEGG Glycan
conn <- mybiodb$getFactory()$createConn('kegg.glycan')

# Terminate instance.
mybiodb$terminate()

KEGG Glycan entry class.

Description

This is the entry class for the KEGG Glycan database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggGlycanEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggGlycanEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.glycan')

# Get an entry
e <- conn$getEntry('G00018')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Pathway database.

Description

The connector class to KEGG Pathway database.

The connector class to KEGG Pathway database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggModuleConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggModuleConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggModuleConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.module')

# Get an entry
e <- conn$getEntry('M00009')

# Terminate instance.
mybiodb$terminate()

KEGG Module entry class.

Description

This is the entry class for KEGG Module database

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggModuleEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggModuleEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.module')

# Get an entry
e <- conn$getEntry('M00009')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Orthology database.

Description

The connector class to KEGG Orthology database.

The connector class to KEGG Orthology database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggOrthologyConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggOrthologyConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggOrthologyConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.orthology')

# Get an entry
e <- conn$getEntry('K12668')

# Terminate instance.
mybiodb$terminate()

KEGG Orthology entry class.

Description

This is the class entry for KEGG Orthology database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggOrthologyEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggOrthologyEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.orthology')

# Get an entry
e <- conn$getEntry('K12668')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Pathway database.

Description

The connector class to KEGG Pathway database.

The connector class to KEGG Pathway database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggPathwayConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggPathwayConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method getReactions()

Retrieves all reactions part of a KEGG pathway. Connects to KEGG databases, and walk through all pathways submitted, and their modules, to find all reactions they are composed of.

Usage
KeggPathwayConn$getReactions(id, drop = TRUE)
Arguments
id

A character vector of entry IDs.

drop

If set to TRUE, returns a single KEGG reaction object instead of a list, if the list contains only one element.

Returns

A list of KEGG reaction objects.

Method convertToOrgPathways()

Takes a list of pathways IDs and converts them to the specified organism, filtering out the ones that do not exist in KEGG.

Usage
KeggPathwayConn$convertToOrgPathways(id, org)
Arguments
id

A character vector of entry IDs.

org

The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.

Returns

A character vector, the same length as 'id', containing the converted IDs.

Method buildPathwayGraph()

Builds a pathway graph in the form of two tables of vertices and edges, using KEGG database.

Usage
KeggPathwayConn$buildPathwayGraph(id, directed = FALSE, drop = TRUE)
Arguments
id

A character vector of KEGG pathway entry IDs.

directed

If set to TRUE, use available direction information to create directed edges, duplicating if necessary the vertices.

drop

If set to TRUE and the output list contains only one element, then the returned value is a single list of two data frames.

Returns

A named list whose names are the pathway IDs, and values are lists containing two data frames named vertices and edges.

Method getPathwayIgraph()

Builds a pathway graph, as an igraph object, using KEGG database.

Usage
KeggPathwayConn$getPathwayIgraph(id, directed = FALSE, drop = TRUE)
Arguments
id

A character vector of KEGG pathway entry IDs.

directed

If set to TRUE, use available direction information to create directed edges, duplicating if necessary the vertices.

drop

If set to TRUE and the output list contains only one element, then the returned value is a single igraph object.

Returns

A list of igraph objects, or an empty list if the igraph library is not available.

Method getDecoratedGraphPicture()

Create a pathway graph picture, with some of its elements colorized.

Usage
KeggPathwayConn$getDecoratedGraphPicture(id, color2ids)
Arguments
id

A KEGG pathway ID.

color2ids

A named list defining colors for entry IDs that are present on the graph. The names of the list are standard color names. The values are character vector of entry IDs.

Returns

An image object or NULL if the package magick is not available.

Method extractPathwayMapShapes()

Extracts shapes from a pathway map image.

Usage
KeggPathwayConn$extractPathwayMapShapes(id, color2ids)
Arguments
id

A KEGG pathway ID.

color2ids

A named list defining colors for entry IDs that are present on the graph. The names of the list are standard color names. The values are character vector of entry IDs.

Returns

A list of BiodbShape objects.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggPathwayConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get connector
conn=mybiodb$getFactory()$createConn('kegg.pathway')

# Retrieve all reactions related to a mouse pathway:
reactions=conn$getReactions('mmu00260')

# Get a pathway graph
graph=conn$buildPathwayGraph('mmu00260')

# Terminate instance.
mybiodb$terminate()

KEGG Pathway entry class.

Description

This is the class entry for KEGG Pathway database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggPathwayEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggPathwayEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.pathway')

# Get an entry
e <- conn$getEntry('map00053')

# Terminate instance.
mybiodb$terminate()

The connector class to KEGG Reaction database.

Description

The connector class to KEGG Reaction database.

The connector class to KEGG Reaction database.

Details

This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodbKegg::KeggConn -> KeggReactionConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
KeggReactionConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggReactionConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.reaction')

# Get an entry
e <- conn$getEntry('R00105')

# Terminate instance.
mybiodb$terminate()

KEGG Reaction entry class.

Description

This is the entry class for KEGG Reation database.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> biodbKegg::KeggEntry -> KeggReactionEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggReactionEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('kegg.reaction')

# Get an entry
e <- conn$getEntry('R00105')

# Terminate instance.
mybiodb$terminate()

A class for representing a rectangle.

Description

A class for representing a rectangle.

A class for representing a rectangle.

Details

This class represents a rectangle, used for graphical representation.

Arguments to the constructor are:

left: Coordinate of left border.

right: Coordinate of right border.

top: Coordinate of top border.

bottom: Coordinate of bottom border.

Super class

biodbKegg::KeggShape -> KeggRect

Methods

Public methods

Inherited methods

Method new()

Initialize new instance.

Usage
KeggRect$new(left, top, bottom, right, ...)
Arguments
left

Coordinate of rectangle's left side.

top

Coordinate of rectangle's top side.

bottom

Coordinate of rectangle's bottom side.

right

Coordinate of rectangle's right side.

...

Additional parameters are passed to super class' initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggRect$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggShape, KeggCircle.

Examples

# Create a rectangle instance
r <- KeggRect$new(left=10, top=10, bottom=20, right=30, color='yellow')

# Draw a rectangle on current image

r$draw()

A class for representing a shape.

Description

A class for representing a shape.

A class for representing a shape.

Details

This abstract class represents a shape, used for graphical representation.

Arguments to the constructor are:

label: A text label to associate with the shape.

color: A color, as a character string.

Methods

Public methods

Method new()

Initialize new instance.

Usage
KeggShape$new(label = NA_character_, color = NA_character_)
Arguments
label

The text label to display.

color

The color to use.

Returns

Nothing.

Method equals()

Test if this shape is the same as another.

Usage
KeggShape$equals(other)
Arguments
other

The other shape to compare with.

Returns

TRUE or FALSE.

Method getLabel()

Gets the label associated with this shape.

Usage
KeggShape$getLabel()
Returns

The label.

Method getColor()

Gets the color associated with this shape.

Usage
KeggShape$getColor()
Returns

The color name as a string.

Method getRgbColor()

Gets the RGB color associated with this shape.

Usage
KeggShape$getRgbColor(alpha = 255)
Arguments
alpha

The value to use for the alpha channel when building the RGB color object.

Returns

The color as an RGB color object.

Method draw()

Draw the shape on the current image.

Usage
KeggShape$draw()
Returns

None.

Method clone()

The objects of this class are cloneable with this method.

Usage
KeggShape$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

KeggRect, KeggCircle.

Examples

# Create a circle instance
c <- KeggCircle$new(x=12, y=5, r=3, label='MyCircle')

# Create a rectangle instance
r <- KeggRect$new(left=10, top=10, bottom=20, right=30, color='yellow')