In [31]:

    

# import library
library(RCy3)
library(igraph)

# import utility
source("../../utility/import.R")

# first, delete existing windows to save memory:
deleteAllWindows(CytoscapeConnection())

# create graph class
g <- new ('graphNEL', edgemode='directed')

edgeDataDefaults(g, attr = "edgeType") <- "undefined"
attr(edgeDataDefaults(g, attr = "edgeType"), "class") <- "STRING"

# Load Data
gal.matrix <- sifDataToMatrix('../sampleData/galFiltered.sif')

# Get NodesVec
gal.table.nodevec <- unique(c(gal.matrix[,1], gal.matrix[,3]))

# add nodes to graph
for(node in gal.table.nodevec){
    g <- graph::addNode(node, g)
}

# get EdgeList and type
gal.table.fromvec <- gal.matrix[,1]
gal.table.type <- gal.matrix[,2]
gal.table.tovec <-  gal.matrix[,3]

for (index in 1:length(gal.table.fromvec)){
    g <- graph::addEdge (gal.table.fromvec[[index]] ,gal.table.tovec[[index]], g)
    edgeData(g, gal.table.fromvec[[index]] ,gal.table.tovec[[index]], "edgeType") <- gal.table.type[[index]]
}

# show it in cytescape
cw <- CytoscapeWindow('vignette', graph=g, overwrite=TRUE)
displayGraph (cw)
layoutNetwork (cw, layout.name='degree-circle')


    

    




Warning message:
In .local(from, to, graph): edges replaced: ‘YPL248C|YML051W’Warning message:
:  使われていないコネクション 4 (../sampleData/galFiltered.sif) を閉じます 





    




[1] "label"
[1] "edgeType"

In [32]:

    

# Select edge by selecting edge directly
# The name format is "geneA (relation) geneB".
selectEdges(cw, paste(gal.table.fromvec[[1]], " (",gal.table.type[[1]], ") ",gal.table.tovec[[1]], sep=""))

# The following code is for showing the result network image.
file.name <- paste (getwd (), 'resultImage' , 'showImageSelectOneEdge' , sep= '/' )
image.type <- 'png'

resource.uri <- paste(cw@uri, 
                      pluginVersion(cw), "networks", as.character(cw@window.id), 
                      paste0("views/first.", image.type), 
                      sep="/")
request.res <- GET(resource.uri, write_disk(paste0(file.name,".", image.type), overwrite = TRUE))


    

In [33]:

    

# Select edges by attribution.
vec = c()
for (index in 1:length(gal.table.fromvec)){
    if(gal.table.type[[index]] == 'pp'){
        vec = c(vec, paste(gal.table.fromvec[[index]], " (",gal.table.type[[index]], ") ", gal.table.tovec[[index]],sep=""))
    }
}
selectEdges (cw, vec)

# The following code is for showing the result network image.
file.name <- paste (getwd (), 'resultImage' ,'showImageSelectEdgeByAttribution' , sep= '/' )
image.type <- 'png'

resource.uri <- paste(cw@uri, 
                      pluginVersion(cw), "networks", as.character(cw@window.id), 
                      paste0("views/first.", image.type), 
                      sep="/")
request.res <- GET(resource.uri, write_disk(paste0(file.name,".", image.type), overwrite = TRUE))


    

In [37]:

    

# select node by its name
selectNodes(cw, "YKR026C")

# The following code is for showing the result network image.
file.name <- paste (getwd(), 'resultImage' , 'showImageSelectOneNode' , sep= '/' )
image.type <- 'png'

resource.uri <- paste(cw@uri, 
                      pluginVersion(cw), "networks", as.character(cw@window.id), 
                      paste0("views/first.", image.type), 
                      sep="/")
request.res <- GET(resource.uri, write_disk(paste0(file.name,".", image.type), overwrite = TRUE))


    

In [38]:

    

# get attributes data
gal.node.attrs <- read.table('../sampleData/galFiltered_node.attrs',stringsAsFactors=FALSE, skip=1)
head(gal.node.attrs)


    

    






V1
V2
V3

	
YKR026C
=      
1      
	
YGL122C
=      
1      
	
YMR146C
=      
1      
	
YDR429C
=      
1      
	
YFL017C
=      
1      
	
YOL123W
=      
1      

In [39]:

    

vac = c()
for (index in 1:length(gal.node.attrs)){
    if(gal.node.attrs[[index,3]] == 1){
        vec = c(vec, gal.node.attrs[[index,1]])
    }
}

# select Nodes by attribution
selectNodes(cw, vec)

# The following code is for showing the result network image.
file.name <- paste (getwd (), 'resultImage' , 'showImageSelectNodesByAttribution' , sep= '/' )
image.type <- 'png'

resource.uri <- paste(cw@uri, 
                      pluginVersion(cw), "networks", as.character(cw@window.id), 
                      paste0("views/first.", image.type), 
                      sep="/")
request.res <- GET(resource.uri, write_disk(paste0(file.name,".", image.type), overwrite = TRUE))


    

In [27]:

    

# Hide selected nodes
hideSelectedEdges(cw)


    

    






NULL

In [28]:

    

# Hide selected nodes
hideSelectedNodes(cw)


    

    




not yet implemented

In [29]:

    

# clear Selection
clearSelection (cw)