mully.Rcheck/mully-Ex.R
In frankkramer-lab/mully: Create, Modify and Visualize Multi-Layered Networks
pkgname <- "mully"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
options(pager = "console")
base::assign(".ExTimings", "mully-Ex.timings", pos = 'CheckExEnv')
base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
base::assign(".format_ptime",
function(x) {
if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
options(OutDec = '.')
format(x[1L:3L], digits = 7L)
},
pos = 'CheckExEnv')
### * </HEADER>
library('mully')
base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
cleanEx()
nameEx("addEdge")
### * addEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addEdge
### Title: Add an edge
### Aliases: addEdge
### ** Examples
g=mully::demo()
addEdge(g,"dr3","g2",attributes=list(name="newEdge"))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("addLayer")
### * addLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addLayer
### Title: Add a layer or a set of layers to a graph
### Aliases: addLayer
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("addNode")
### * addNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addNode
### Title: Add a node with assigned layer and attributes to a graph
### Aliases: addNode
### ** Examples
g=mully::demo()
attributes=list("specie"="Homo Sapiens")
addNode(g = g,nodeName = "g3",layerName = "Gene",attributes = attributes)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("exportCSV")
### * exportCSV
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: exportCSV
### Title: Export mully into CSV files
### Aliases: exportCSV
### ** Examples
## Not run:
##D g=mully::demo()
##D exportCSV(g)
## End(Not run)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("exportCSV", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getEdgeAttributes")
### * getEdgeAttributes
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getEdgeAttributes
### Title: Get the attributes of the edges connecting two nodes
### Aliases: getEdgeAttributes
### ** Examples
g=mully::demo()
#Print all Edges
getEdgeAttributes(g)
#Get a Single Edge
getEdgeAttributes(g,"d2","g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getEdgeAttributes", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getIDEdge")
### * getIDEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getIDEdge
### Title: Get the ids of the edges connecting two nodes
### Aliases: getIDEdge
### ** Examples
g=mully::demo()
getIDEdge(g,"d2","dr1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getIDEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getIDNode")
### * getIDNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getIDNode
### Title: Get the id of a node
### Aliases: getIDNode
### ** Examples
g=mully::demo()
getIDNode(g,"g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getIDNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getLayer")
### * getLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getLayer
### Title: Get the nodes on a layer in a graph
### Aliases: getLayer
### ** Examples
g = mully::demo()
getLayer(g,"gene")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getLayersCount")
### * getLayersCount
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getLayersCount
### Title: Get the number of layers in a graph
### Aliases: getLayersCount
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
getLayersCount(g)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getLayersCount", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getNode")
### * getNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getNode
### Title: Get a node from a graph
### Aliases: getNode
### ** Examples
g=mully::demo()
getNode(g,"g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getNodeAttributes")
### * getNodeAttributes
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getNodeAttributes
### Title: Get the attributes of a node
### Aliases: getNodeAttributes
### ** Examples
g=mully::demo()
getNodeAttributes(g,layerByName = TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getNodeAttributes", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("isLayer")
### * isLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: isLayer
### Title: Verify if the layer exists in a graph
### Aliases: isLayer
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
isLayer(g,"Drug")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("isLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("mully")
### * mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: mully
### Title: Create an empty multilayered graph
### Aliases: mully
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("plot.mully")
### * plot.mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: plot.mully
### Title: Plot the graph in 2D
### Aliases: plot.mully
### ** Examples
g=mully::demo()
plot(g,"Scaled")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("plot.mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("plot3d")
### * plot3d
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: plot3d
### Title: Plot the graph in 3D using rgl
### Aliases: plot3d
### ** Examples
g=mully::demo()
labels=getNodeAttributes(g)$name
plot3d(g, layers=TRUE, vertex.label=labels,edge.width=6)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("plot3d", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("print.mully")
### * print.mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: print.mully
### Title: Print function
### Aliases: print.mully
### ** Examples
g=mully::demo()
print(g)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("print.mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeEdge")
### * removeEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeEdge
### Title: Delete an edge
### Aliases: removeEdge
### ** Examples
g=mully::demo()
removeEdge(g,"dr1","d2",multi=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeLayer")
### * removeLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeLayer
### Title: Delete a layer or a set of layers from a graph
### Aliases: removeLayer
### ** Examples
g = mully::demo()
removeLayer(g,"gene",trans=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeNode")
### * removeNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeNode
### Title: Delete a node or a set of nodes from a graph
### Aliases: removeNode
### ** Examples
g=mully::demo()
removeNode(g,"dr1",trans=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
### * <FOOTER>
###
cleanEx()
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
frankkramer-lab/mully documentation built on Feb. 25, 2023, 2:40 a.m.
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pkgname <- "mully"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
options(pager = "console")
base::assign(".ExTimings", "mully-Ex.timings", pos = 'CheckExEnv')
base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
base::assign(".format_ptime",
function(x) {
if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
options(OutDec = '.')
format(x[1L:3L], digits = 7L)
},
pos = 'CheckExEnv')
### * </HEADER>
library('mully')
base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
cleanEx()
nameEx("addEdge")
### * addEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addEdge
### Title: Add an edge
### Aliases: addEdge
### ** Examples
g=mully::demo()
addEdge(g,"dr3","g2",attributes=list(name="newEdge"))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("addLayer")
### * addLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addLayer
### Title: Add a layer or a set of layers to a graph
### Aliases: addLayer
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("addNode")
### * addNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: addNode
### Title: Add a node with assigned layer and attributes to a graph
### Aliases: addNode
### ** Examples
g=mully::demo()
attributes=list("specie"="Homo Sapiens")
addNode(g = g,nodeName = "g3",layerName = "Gene",attributes = attributes)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("addNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("exportCSV")
### * exportCSV
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: exportCSV
### Title: Export mully into CSV files
### Aliases: exportCSV
### ** Examples
## Not run:
##D g=mully::demo()
##D exportCSV(g)
## End(Not run)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("exportCSV", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getEdgeAttributes")
### * getEdgeAttributes
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getEdgeAttributes
### Title: Get the attributes of the edges connecting two nodes
### Aliases: getEdgeAttributes
### ** Examples
g=mully::demo()
#Print all Edges
getEdgeAttributes(g)
#Get a Single Edge
getEdgeAttributes(g,"d2","g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getEdgeAttributes", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getIDEdge")
### * getIDEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getIDEdge
### Title: Get the ids of the edges connecting two nodes
### Aliases: getIDEdge
### ** Examples
g=mully::demo()
getIDEdge(g,"d2","dr1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getIDEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getIDNode")
### * getIDNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getIDNode
### Title: Get the id of a node
### Aliases: getIDNode
### ** Examples
g=mully::demo()
getIDNode(g,"g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getIDNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getLayer")
### * getLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getLayer
### Title: Get the nodes on a layer in a graph
### Aliases: getLayer
### ** Examples
g = mully::demo()
getLayer(g,"gene")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getLayersCount")
### * getLayersCount
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getLayersCount
### Title: Get the number of layers in a graph
### Aliases: getLayersCount
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
getLayersCount(g)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getLayersCount", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getNode")
### * getNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getNode
### Title: Get a node from a graph
### Aliases: getNode
### ** Examples
g=mully::demo()
getNode(g,"g1")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("getNodeAttributes")
### * getNodeAttributes
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: getNodeAttributes
### Title: Get the attributes of a node
### Aliases: getNodeAttributes
### ** Examples
g=mully::demo()
getNodeAttributes(g,layerByName = TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("getNodeAttributes", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("isLayer")
### * isLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: isLayer
### Title: Verify if the layer exists in a graph
### Aliases: isLayer
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
g = addLayer(g, c("Gene", "Drug", "Disease"))
isLayer(g,"Drug")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("isLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("mully")
### * mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: mully
### Title: Create an empty multilayered graph
### Aliases: mully
### ** Examples
g = mully("MyFirstMully",direct = FALSE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("plot.mully")
### * plot.mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: plot.mully
### Title: Plot the graph in 2D
### Aliases: plot.mully
### ** Examples
g=mully::demo()
plot(g,"Scaled")
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("plot.mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("plot3d")
### * plot3d
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: plot3d
### Title: Plot the graph in 3D using rgl
### Aliases: plot3d
### ** Examples
g=mully::demo()
labels=getNodeAttributes(g)$name
plot3d(g, layers=TRUE, vertex.label=labels,edge.width=6)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("plot3d", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("print.mully")
### * print.mully
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: print.mully
### Title: Print function
### Aliases: print.mully
### ** Examples
g=mully::demo()
print(g)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("print.mully", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeEdge")
### * removeEdge
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeEdge
### Title: Delete an edge
### Aliases: removeEdge
### ** Examples
g=mully::demo()
removeEdge(g,"dr1","d2",multi=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeEdge", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeLayer")
### * removeLayer
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeLayer
### Title: Delete a layer or a set of layers from a graph
### Aliases: removeLayer
### ** Examples
g = mully::demo()
removeLayer(g,"gene",trans=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeLayer", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
cleanEx()
nameEx("removeNode")
### * removeNode
flush(stderr()); flush(stdout())
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: removeNode
### Title: Delete a node or a set of nodes from a graph
### Aliases: removeNode
### ** Examples
g=mully::demo()
removeNode(g,"dr1",trans=TRUE)
base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("removeNode", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
### * <FOOTER>
###
cleanEx()
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
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