Using igraph, some basic i/o and plotting.

Graph_Explorations.R

#' ---
#' title: "Graph_Explorations.R"
#' author: "Matt Pettis (Matthew.Pettis@gmail.com)"
#' date: "`r Sys.Date()`"
#' output:
#'   html_document:
#'     toc: true
#'     toc_depth: 3
#'     code_folding: hide
#' editor_options:
#'   chunk_output_type: console
#' ---
#'


#+message=F,warning=F

#;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
#;; Setup

library(tidygraph)
library(DiagrammeR)
library(DiagrammeRsvg)
library(igraph)
# library(janitor)
library(glue)
# library(purrr)
# library(lubridate)
library(tidyverse)
#;; https://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html
library(Rgraphviz)




#' # Graphs on a simple tree, directed
#' 
#' The label, color, and shape attributes added to the nodes dictate those
#' properties when the graph is plotted.
#' 
#+
#;; Make a tree igraph
nodesTree1_df <-
    tribble(
        ~name, ~label, ~color, ~shape
        , "A", "root", "red", "circle"
        , "B", "L1-1\nmore text", "yellow", "rectangle"
        , "C", "L1-2", "yellow", "rectangle"
        , "D", "L1-1-1", "green", "none"
        , "E", "L1-1-2", "green", "none"
        , "F", "L1-1-3", "green", "none"
        , "G", "L1-2-1", "green", "none"
        , "H", "L1-2-2", "green", "none"
    )
edgesTree1_df <-
    tribble(
        ~from, ~to
        , "A", "B"
        , "A", "C"
        , "B", "D"
        , "B", "E"
        , "B", "F"
        , "C", "G"
        , "C", "H"
    )

#;; Make the graph
gTree1 <- graph_from_data_frame(d = edgesTree1_df %>%
                               select(from, to, everything())
                           , directed = TRUE
                           , vertices = nodesTree1_df %>%
                               select(name, everything()))

#' ## Extract the parts
#' 
#' If you also import tibble, or parts of the tidyverse, you have to explicitly
#' call `igraph::as_data_frame()`, because you'll see this message:
#' 
#'     dplyr::as_data_frame() masks tibble::as_data_frame(), igraph::as_data_frame()
#' 
#' when you load the libraries.
#' 
#' See: https://igraph.org/r/html/latest/graph_from_data_frame.html
#+
igraph::as_data_frame(gTree1, what="vertices")
igraph::as_data_frame(gTree1, what="edges")

#' ## Plot it
#' 
#' Default plot isn't what we want, doesn't plot like a tree.
#+
plot(gTree1)

#' But we can control options.
#' 
#' See: https://igraph.org/r/html/latest/plot.common.html
#+
plot(gTree1, layout=layout_as_tree)


#' But we can control these options globally as well.  We have to prefix global
#' options with 'plot.'  This will do the same thing:
#' 
#' ```
#' igraph_options(plot.layout=layout_as_tree)
#' plot(gTree1)
#' ```
#' 

#' ## Save plot
#' Save as named svg file.
#' 
#' See: https://stackoverflow.com/questions/48796194/export-r-plot-via-svg-without-zooming
#' 
#' ````
#' svg(here::here("dat", "tree1.svg"))
#' plot(gTree1, layout=layout_as_tree)
#' dev.off() %>% invisible()
#' ````
#' 


#' ## Convert to graphviz and using it
#' See:
#' 
#' - https://igraph.org/r/html/latest/write_graph.html
#' 
#' Not helpful, but here:
#' 
#' See:
#' 
#' - https://rdrr.io/cran/DiagrammeR/man/from_igraph.html
#' - https://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html
#' 
#+ 
#;; Save as dot file
write_graph(gTree1, here::here("dat", "tree1.dot"), format="dot")

#;; Read in and render with graphviz engine
DiagrammeR:::grViz(here::here("dat", "tree1.dot"))


#;; Read in dot file to Ragraph object
#;; See: https://support.bioconductor.org/p/48598/
rgvzTree1 <-
    Rgraphviz::agread(here::here("dat", "tree1.dot"))
# renderGraph(rgvzTree1)


#;; Create a graphNEL object

#;; Convert to Ragraph object
#;; https://www.bioconductor.org/packages/release/bioc/manuals/Rgraphviz/man/Rgraphviz.pdf
#;; https://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
agopen(randomGraph(letters[1:10], 1:4, 0.2), "g1")

#;; This works!!!
#;; Try to convert iGraph -> graphNEL -> Ragraph object.
rgvz2Tree1 <-
    igraph::as_graphnel(gTree1) %>%
    agopen("gTree1")


#;; Some plotting
plot(rgvz2Tree1)

plot(rgvz2Tree1, attrs=list(graph=list(rankdir="LR")))
plot(rgvz2Tree1, attrs=getDefaultAttrs())

g1 <-
    plot(randomGraph(letters[1:10], 1:4, 0.2))
plot(g1, attrs=getDefaultAttrs())