make_mgraph: make graph from various data

In zgzhao/gmetab: syzMetab: R package for metabolic network analysis

Description

Make metabolic graph from various type of data: KDataSet, ReactionSet, ReactionList, list, KOs or other xgraph object.

Usage

- make_mgraph(object, ...): from KDataSet, ResctionSet, ReactionList, list or character vector (kos)
- make_rgraph(object, ...): from KDataSet, ResctionSet, ReactionList or character vector (kos)
- make_ggraph(object, ...): from KDataSet, ResctionSet, ReactionList or character vector (kos)
- make_bgraph(object, ...): from mgraph or stcuts (refer to make_stcuts)

Arguments

object	KDataSet, ReactionSet ReactionList, character vector or list.
...	additional parameters depends on "object" org: organism/species indentifier, parameter for "object" without organism info such as ReactionList and list d.path: character, refer to KEGG_get for detail. Used when "object" is a character vector (kos).

Details

Metabolic network can be represented by metabolite, reaction, gene graph or st-cuts of gene sets.

• make_mgraph (make metabolite graph): nodes are metabolites and edges are reactions identified by gene sets

• make_rgraph (make reaction graph): nodes are reactions

• make_ggraph (make gene graph): nodes are genes

• make_bgraph (make bipartite graph): derived from st-cuts of mgraph. Nodes are genes and st-cuts of gene sets. Edges are links between gene sets and the genes included.

Author(s)

zhao

Examples

## NOT RUN
library(syzMetab)
pp <- make_kdset("ko00010", d.path="KEGG")
make_mgraph(pp)
make_mgraph(Reactions(pp), org="ko")
make_mgraph("ko00010")
gm <- make_mgraph(c("ko00010", "ko00020"))
plot(gm)
gr <- make_rgraph("ko00010")
plot(gr)
gg <- make_ggraph("ko00010")
plot(gg)
chem1 <- c("C00031", "C00221", "C00267", "C01172", "C01451", "C06186")
chem2 <- "C00022"
gb <- make_bgraph(gm, s=chem1, t=chem2, minimal=FALSE)
plot(gb)

zgzhao/gmetab documentation built on Dec. 23, 2021, 9:17 p.m.