interactive.omics.network: Interaction Omics Network Object

In montilab/bieulergy: Interactive analysis of multi-omics regulatory networks

Interaction Omics Network Object

Description

Interaction Omics Network Object

Interaction Omics Network Object

Public fields

ig

An igraph object

pca

Dimensionality reduction on node measures

nodes

A data frame of labeled nodes

edges

A data frame of undirected edges

properties

A list of graph-level properties Init

Methods

Public methods

• interactive.omics.network$new()

• interactive.omics.network$print()

• interactive.omics.network$init.properties()

• interactive.omics.network$init.nodes()

• interactive.omics.network$init.edges()

• interactive.omics.network$get.symbols()

• interactive.omics.network$get.interactors()

• interactive.omics.network$get.subnetwork()

• interactive.omics.network$plt.subnetwork()

• interactive.omics.network$clone()

---

Method new()

Usage

interactive.omics.network$new(
  ig,
  symbols = NULL,
  graph.measures = c("nodes", "edges", "density", "clustering"),
  node.measures = c("degree", "eigen", "betweenness", "stress"),
  quiet = TRUE
)

Arguments

ig

An undirected igraph object

symbols

A mapping of node identifiers to symbols

graph.measures

A vector of graph measures to compute

node.measures

A vector of node measures to compute

quiet

Use true to silence messages

Returns

A new network object

---

Method print()

Print network information

Usage

interactive.omics.network$print()

Returns

NULL

---

Method init.properties()

Computes graph-level properties

Usage

interactive.omics.network$init.properties(measures = c(), quiet = TRUE)

Arguments

measures

A vector of measures to compute

quiet

Use true to silence messages

Returns

NULL

---

Method init.nodes()

Computes node-level properties

Usage

interactive.omics.network$init.nodes(
  symbols = NULL,
  measures = c(),
  quiet = TRUE
)

Arguments

symbols

A mapping of node identifers to symbols

measures

A vector of measures to compute

quiet

Use true to silence messages

Returns

NULL

---

Method init.edges()

Computes edge-level properties

Usage

interactive.omics.network$init.edges()

Returns

NULL

---

Method get.symbols()

Maps ids to symbols

Usage

interactive.omics.network$get.symbols(ids)

Arguments

ids

A vector of node identifiers

Returns

A vector of symbols

---

Method get.interactors()

Get interactors

Usage

interactive.omics.network$get.interactors(
  ids,
  degree = 1,
  remove.ids = TRUE,
  use.symbols = FALSE
)

Arguments

ids

Node identifiers

degree

Edge degree to include in subset

remove.ids

Include original ids

use.symbols

Return node symbols instead of ids

Returns

A vector of interactors

---

Method get.subnetwork()

Get subnetwork

Usage

interactive.omics.network$get.subnetwork(
  ids,
  degree = 1,
  indirect.edges = FALSE
)

Arguments

ids

Node identifiers

degree

Edge degree to include in subset

indirect.edges

Include edges between non-queried nodes

Returns

A list of nodes and edges

---

Method plt.subnetwork()

Plot subnetwork

Usage

interactive.omics.network$plt.subnetwork(
  ids,
  degree = 1,
  indirect.edges = FALSE,
  use.symbols = FALSE,
  node.color = NULL,
  node.border = NULL,
  node.size = NULL,
  node.shape = NULL,
  layout = "layout_nicely",
  node.attr = list(),
  edge.attr = list(),
  ...
)

Arguments

ids

Node identifiers

degree

Edge degree to include in subset

indirect.edges

Include edges between non-queried nodes

use.symbols

Show node symbols instead of ids

node.color

Node column to determine node background color

node.border

Node column to determine node border color

node.size

Node column to determine node size

node.shape

Node column to determine node shape

layout

An igraph layout

node.attr

Node attributes passed to 'visNodes()'

edge.attr

Edge attributes passed to 'visEdges()'

...

Additional keyword arguments passed to 'visNetwork()'

Returns

A visNetwork object

---

Method clone()

The objects of this class are cloneable with this method.

Usage

interactive.omics.network$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

montilab/bieulergy documentation built on March 25, 2022, 3:40 p.m.