05-stringGraph: Class '"StringGraph"'

In SVAlignR: Recovering Structure of Long Molecules from Structural Variation Data

Class "StringGraph"

Description

The StringGraph class is used to represent graphs that arise from strings reprsenting long-read breakpoint sequences. The basic examples are: (1) "Motif Graphs" where the edges are subtring relations, and (2) "Decomposition Graphs" where the edges are restricted subtring relations that decompose a long read.

Usage

MotifGraph(motifNodes, alfa, name = "motif")
DecompositionGraph(decomp, alfa, motifNodes, name = "decomp")
exportSG(sg, outdir = ".")
## S4 method for signature 'StringGraph,ANY'
plot(x, y, ...)

Arguments

motifNodes	A list of node names and counts, separated by length. In particular, motifNodes[[L]] should contain the nodes of length L.
alfa	A Cipher object.
name	A character vector of length one.
decomp	A decomposition object; see details.
sg	An object of the StringGraph class.
outdir	A chara cter string, the name of the output directory.
x	An object of the StringGraph class.
y	Anything; it is ignored.
...	Extra graphical parameters.

Value

The MotifGraph and DecompositionGraph functions return a new object of the StringGraph class. The plot method and exportSG functions return nothing and are called for their side effects.

Objects from the Class

Objects should be defined using the MotifGraph or DecompositionGraph constructor. You typically pass in a "motifNodes" object, which is a list of sequence-strings separated by length, along with some auxiliary information.

Slots

name:

A character vector of length one.

edgelist:

A matrix representing a graph as a list of edges.

nodelist:

A matrix representing the nodes of the graph, along with their properties.

graph:

An igraph object.

layout:

A matrix containing x-y locations for the nodes.

Note

Attempting to manipulate a StringGraph object using text containing NAs, missing values, or previously unknown symbols will result in an error.

Author(s)

Kevin R. Coombes <[e-mail]>

SVAlignR documentation built on Sept. 4, 2025, 3:01 p.m.