In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

Examples pulled from Network Visualization with R, Polnet 2016 by Katya Ognyanova.

suppressPackageStartupMessages({
  library(RColorBrewer)
  library(readr)
  library(dplyr)
  library('visNetwork') 
})

Here use visNetwork package. visNetwork enables setting graphic properties as node or edge attributes by adding them as data columns before calling visNetwork(). See available options with:

?visNodes
?visEdges

For more information, see:

?visOptions # available options 
?visLayout  # available layouts
?visGroups  # using node groups
?visLegend  # adding a legend

Basic visNetwork with Dataset 1

nodes <- 
   read_csv(system.file("extdata", "ShinyLogicNodes.csv", package = "qtl2shiny")) %>%
  mutate(id = node) %>%
  select(-node)
links <- 
   read_csv(system.file("extdata", "ShinyLogicEdges.csv", package = "qtl2shiny")) %>%
  mutate(from = source,
         to = target) %>%
  select(-source,-target)

Open dataset 1 with visNetwork.

visNetwork(nodes, links, width="100%", height="400px", main="Network!")

Changing some node parameters:

shape (ellipse, circle, database, box, text, image, circularImage, diamond, dot, star, triangle, triangleDown, square, icon)
color.background (node color)
color.border (frame color)
color.highlight (color on mouse click)
color.hover (color on mouseover)

nodes$shape <- "dot"  
nodes$shadow <- TRUE # Nodes will drop shadow
nodes$title <- nodes$id # Text on click
nodes$label <- nodes$logic # Node label
#nodes$size <- nodes$audience.size # Node size
nodes$borderWidth <- 2 # Node border width

nodes$color.background <- c("skyblue", "tomato", "slategrey", "gold")[factor(nodes$logic)]
nodes$color.border <- "black"
nodes$color.highlight.background <- "orange"
nodes$color.highlight.border <- "darkred"

visNetwork(nodes, links)

Set up hover option.

nodes$color.hover.background <- "green"
visNetwork(nodes, links) %>%
 visInteraction(hover = TRUE)

Change visual properties of edges.

#links$width <- 1 + links$weight/8 # line width
links$color <- "gray"    # line color  
links$arrows <- "middle" # arrows: 'from', 'to', or 'middle'
links$smooth <- FALSE    # should the edges be curved?
links$shadow <- FALSE    # edge shadow

visNetwork(nodes, links)

visNetwork offers a number of other options in the visOptions() function. For instance, highlight all neighbors of a selected node (highlightNearest), or add a drop-down menu to select groups of nodes (selectedBy). The groups are based on data columns such as type label.

## nodes must be a data frame, not tbl_df.
visNetwork(as.data.frame(nodes), links) %>%
  visOptions(highlightNearest = TRUE, 
             selectedBy = "type.label")