subset_graph: subset xgraph

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

Description

Subset graph with given sources (primary substrates) and targets (products)

Usage

subset_graph(object, s, t, clean = FALSE)

Arguments

object	graph object
s	source nodes
t	target nodes

Details

• In "setorg_graph", reactions without mapping genes are labeled with "absent". This function removes the "absent" links in the graph.

• After setting sources and targets, nodes to sources or from targets should be removed.

• Nodes not accessed by sources or targets should be removed also.

• If clean=TRUE, nodes and edges not in paths from sources to targets are further removed by calling all_spaths_list.

Value

graph object

Author(s)

ZG Zhao

Examples

## NOT RUN
library(syzMetab)
gm <- make_mgraph("ko00010")
chem1 <- c("C00031", "C00221", "C00267", "C01172", "C01451", "C06186")
chem2 <- "C00022"
gx <- subset_graph(gm, s=chem1, t=chem2)
par(mfrow=c(2,1))
plot(gm)
plot(gx)

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