Examples
Create network Edge List and Node Attributes
library(networkly)
library(plotly)
#set up network structure
conn<-1 # average number of conenctions per variable
nodes<-10 # number of variables
net_size<-conn*nodes
edge_type<-2 # number of diffrent connections
#color/size
set.seed(555)
id<-factor(sample(1:edge_type,net_size,replace = TRUE))
id2<-factor(sample(1:10,nodes,replace = TRUE))
edge.list<-data.frame(source=sample(1:nodes,net_size,replace=TRUE),
target=sample(1:nodes,net_size,replace=TRUE),
color=rainbow(edge_type)[id],
size=sample(seq(1,10,length.out=10),edge_type,replace=TRUE)[id],
names=letters[id],stringsAsFactors = FALSE)
node.data<-data.frame(color=sample(rainbow(10),nodes,replace=TRUE)[id2],
size=sample(seq(5,15,length.out=10),nodes,replace=TRUE)[id2],
names=sample(LETTERS[1:5],nodes,replace=TRUE)[id2],stringsAsFactors = FALSE)
Edge List describing network connections
head(edge.list)
## source target color size names
## 1 4 5 #FF0000FF 8 a
## 2 1 3 #00FFFFFF 5 b
## 3 3 7 #00FFFFFF 5 b
## 4 3 3 #00FFFFFF 5 b
## 5 2 3 #00FFFFFF 5 b
## 6 6 3 #FF0000FF 8 a
Node Attributes describing variables
head(node.data)
## color size names
## 1 #FF0000FF 8.333333 C
## 2 #0066FFFF 6.111111 A
## 3 #FF9900FF 9.444444 D
## 4 #FF9900FF 9.444444 D
## 5 #FF9900FF 15.000000 B
## 6 #CC00FFFF 9.444444 C
Create 2D network
layout<-"fruchtermanreingold" #see networkly::get_network for 2D and 3D options
#net params
type<-"2d"
color<-'color'
size<-'size'
name<-'names'
#create network objects
obj<-get_network(edge.list,type=type,layout=layout)
net<-c(get_edges(obj,color=color,width=size,name=name,type=type,hoverinfo="none",showlegend=FALSE),get_nodes(obj,node.data,color=color,size=size,name=name,type=type,hoverinfo="name",showlegend=FALSE))
#add legend
legend<-format_legend(obj,node.data=node.data)
net<-c(net,c(get_edges(legend,color=color,width=size,name=name,type=type,hoverinfo="none",showlegend=TRUE),get_nodes(legend,node.data=legend$node.data,color=color,size=size,name=name,type=type,hoverinfo="name",showlegend=TRUE)))
net<-shiny_ly(net) # works in or out of shiny
#add layout options
layout(net,
xaxis = list(title = "", showgrid = FALSE, showticklabels = FALSE, zeroline = FALSE, hoverformat = '.2f'),
yaxis = list(title = "", showgrid = FALSE, showticklabels = FALSE, zeroline = FALSE, hoverformat = '.2f'))
Create 3D network
#net params
type<-"3d"
#create network objects
obj<-get_network(edge.list,type=type,layout=layout)
net<-c(get_edges(obj,color=color,width=size,name=name,type=type,hoverinfo="none",showlegend=FALSE),get_nodes(obj,node.data,color=color,size=size,name=name,type=type,hoverinfo="name",showlegend=FALSE))
#add legend
legend<-format_legend(obj,node.data=node.data)
net<-c(net,c(get_edges(legend,color=color,width=size,name=name,type=type,hoverinfo="none",showlegend=TRUE),get_nodes(legend,node.data=legend$node.data,color=color,size=size,name=name,type=type,hoverinfo="name",showlegend=TRUE)))
net<-shiny_ly(net)
#add layout options
layout(net,
scene = list(showlegend=TRUE,
yaxis=list(showgrid=FALSE,showticklabels=FALSE,zeroline=FALSE,title=""),
xaxis=list(showgrid=FALSE,showticklabels=FALSE,zeroline=FALSE,title=""),
zaxis=list(showgrid=FALSE,showticklabels=FALSE,zeroline=FALSE,title="")))
Shiny
ui.R
shinyUI(bootstrapPage(
plotlyOutput("network")
))
server.R
shinyServer(function(session,input, output) {
output$network<-renderPlotly({
#network creation script goes here
#see above for how to create 2d or 3d networks
shiny_ly(net)
})
})
Run Demo App
networklyShiny()
Limitations
To allow edge widths in 2D and 3D networks and to properly render edge paths in 3D networks each edge element is an independent list item. The shown edge and node legends are place holders which do not correctly show or hide components. This can be changed during the network creation procces by using showlegend=TRUE and not creating a place holder legend as shown below. For 2D networks edge segments can be renderd from a vector with intermittent NAs e.g. x/y/z = source1 target1 NA source2 target2 this currently does not work for 3D networks.
net<-c(get_edges(obj,color=color,width=size,name=name,type=type,hoverinfo="none",showlegend=TRUE),get_nodes(obj,node.data,color=color,size=size,name=name,type=type,hoverinfo="name",showlegend=TRUE))
shiny_ly(net)
About
updated 2016-02-28
sessionInfo()
## R version 3.2.3 (2015-12-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 8.1 x64 (build 9600)
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotly_2.4.4 ggplot2_2.0.0 networkly_0.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.3 knitr_1.12 magrittr_1.5 network_1.12.0
## [5] munsell_0.4.3 colorspace_1.2-6 R6_2.1.2 stringr_1.0.0
## [9] httr_1.1.0 plyr_1.8.3 dplyr_0.4.1 tools_3.2.3
## [13] parallel_3.2.3 grid_3.2.3 gtable_0.1.2 sna_2.3-2
## [17] DBI_0.3.1 htmltools_0.3 yaml_2.1.13 assertthat_0.1
## [21] digest_0.6.9 gridExtra_2.0.0 formatR_1.2.1 viridis_0.3.2
## [25] htmlwidgets_0.5 base64enc_0.1-3 evaluate_0.8 rmarkdown_0.9
## [29] stringi_1.0-1 scales_0.3.0 jsonlite_0.9.19