index.Rmd

--- 
title: "Metabolic Modelling Techniques"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
bibliography: [refs.bib, packages.bib]
biblio-style: apalike
link-citations: yes
---
# Overview

```{r echo=FALSE}
temp <- purrr::quietly(library)(tidyverse)
temp <- purrr::quietly(library)(yaml)
temp <- purrr::quietly(library)(visNetwork)

treefun_character <- function(x){
  return(list(name = x, children = list()))
}

treefun_onelist <- function(x){
  list(name = names(x),
       children = treefun(x[[1]]))
}

treefun <- function(x){
  c(x %>% keep(is_list) %>% map(treefun_onelist),
    x %>% keep(is_character) %>% map(treefun_character))
}

getNodes <- function(x){
  bind_rows(tibble::as_data_frame(x[names(x)!='children']) %>%
              mutate(nchildren = length(x$children)), 
            map_df(x$children %>% keep(is_list), getNodes)
  )
}

getEdges <- function(x){
  if(length(x$children)==0){return(NULL)}
  
  bind_rows(data_frame(from = x$name, to = x$children %>% map_chr('name')),
            map_df(x$children, getEdges))
}

tax <- read_file('data/taxonomy.yaml') %>%
  yaml.load() %>%
  treefun_onelist()

visNetwork(nodes = getNodes(tax) %>% 
             mutate(id=name, 
                    title=name, 
                    label=name,
                    shape = if_else(nchildren>=1, 'box', 'text')),
           edges = getEdges(tax),
           height = '1000px',
           width = '750px') %>%
  visHierarchicalLayout(direction = 'LR', sortMethod = 'directed', levelSeparation=1000) %>%
  visPhysics(solver='hierarchicalRepulsion', 
             hierarchicalRepulsion = list(nodeDistance = 150, 
                                          springLength = 150, 
                                          springConstant= 0.01, 
                                          damping=0.5
             )
  ) %>%
  visNodes(font = list(size = 60, face = 'arial'), color = list(background = 'white')) %>%
  visEdges(smooth = list(enabled=TRUE, type='continuous')) %>%
  visExport(type='pdf')

```