xConverter: Function to convert an object between graph classes

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Function to convert an object between graph classes

Description

xConverter is supposed to convert an object between classes "igraph", "dgCMatrix", "dtree", "lol", and "json".

Usage

xConverter(
obj,
from = c("igraph", "dgCMatrix", "dtree", "lol", "json"),
to = c("dgCMatrix", "igraph", "dtree", "lol", "json", "igraph_tree"),
verbose = TRUE
)

Arguments

obj	an object of class "igraph", "dgCMatrix", "dtree", "lol", and "json"
from	a character specifying the class converted from. It can be one of "igraph", "dgCMatrix", "dtree", "lol", "json"
to	a character specifying the class converted to. It can be one of "igraph", "dgCMatrix", "dtree", "lol", "json" and "igraph_tree"
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

an object of class "igraph", "dgCMatrix", "dtree", "lol", or "json".

Note

Conversion is supported directly: 1) from 'igraph' to "dgCMatrix","dtree","lol","json","igraph_tree"; 2) from 'dgCMatrix' to "igraph"; 3) from 'dtree' to "igraph","lol","json"; 4) from 'lol' to "dtree","json"; 5) from 'json' to "lol","dtree". In summary: "dgCMatrix" – "igraph" (hub) – "dtree" (hub) – "lol" – "json". Note: 1) igraph –as.igraph– phylo –as.hclust/as.phylo– hclust –as.dendrogram/as.hclust– dendro; 2) igraph –ggraph::den_to_igraph– dendro

See Also

xRDataLoader

Examples

# generate a ring graph
g <- make_ring(10, directed=TRUE)

# convert the object from 'igraph' to 'dgCMatrix' class
xConverter(g, from='igraph', to='dgCMatrix')

## Not run: 
# Conversion between 'dgCMatrix' and 'igraph'
# ig.EF (an object of class "igraph" storing as a directed graph)
g <- xRDataLoader('ig.EF')
g

# convert the object from 'igraph' to 'dgCMatrix' class
s <- xConverter(g, from='igraph', to='dgCMatrix')
s[1:10,1:10]

# convert the object from 'dgCMatrix' to 'igraph' class
ig <- xConverter(s, from="dgCMatrix", to="igraph")
ig

##############
g <- make_graph("Zachary")

# from 'igraph' to "dtree","lol","json"
dtree <- xConverter(g, from='igraph', to='dtree')
lol <- xConverter(g, from='igraph', to='lol')
json <- xConverter(g, from='igraph', to='json')

# from "lol","json" to 'dtree' 
dtree <- xConverter(lol, from='lol', to='dtree')
dtree <- xConverter(json, from='json', to='dtree')

# from 'dtree' to "igraph"
g <- xConverter(dtree, from='dtree', to='igraph')

# force 'igraph' to a tree
gtree <- xConverter(g, from='igraph', to='igraph_tree')

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.