Plot multible networkD3-plots (Sanky) in a for loop

[weldbild]

Hello,

I am working on an Markdown project, where i need to plot multible networkD3 Sanky-network-plots in a for loop. But when i knit the poject to an html the plots wont show in the document. The wired part is when i call the function which generates the Sanky-Plot outside the for loop the results are shown.

Here i have made a very simple version of my code. (NOTE here the function MakeSanky dose nothing special and just returns the same plot for each i, for my case the function is in a different file with several parameters):

---
output:
  html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)

library(networkD3)
library(data.table)
library(dplyr)
library(tidyverse)
library(ggplot2)
library(knitr)


MakeSanky <- function(year){
  links <- data.frame(
  source=c("group_A","group_A", "group_B", "group_C", "group_C", "group_E"), 
  target=c("group_C","group_D", "group_E", "group_F", "group_G", "group_H"), 
  value=c(2,3, 2, 3, 1, 3)
  )
 
  # From these flows we need to create a node data frame: it lists every entities involved in the flow
  nodes <- data.frame(
    name=c(as.character(links$source), 
    as.character(links$target)) %>% unique()
  )
   
  # With networkD3, connection must be provided using id, not using real name like in the links dataframe.. So we need to reformat it.
  links$IDsource <- match(links$source, nodes$name)-1 
  links$IDtarget <- match(links$target, nodes$name)-1
   
  # Make the Network
  p <- sankeyNetwork(Links = links, Nodes = nodes,
                Source = "IDsource", Target = "IDtarget",
                Value = "value", NodeID = "name", 
                sinksRight=FALSE)
  return(p)
}

---

title: "Test:"
output: bookdown::html_document2
editor_options:
chunk_output_type: console

\newpage

year <- c("2014", "2015", "2018")

print("Here the plots are missing")
for(i in year){
  cat(i)
  cat('\n\n')
  g <- MakeSanky(i)
  print(g)
  cat('\n\n')
}
print("This plots are shown correct")
MakeSanky(year[1])
MakeSanky(year[2])
MakeSanky(year[3])

As you can see if i call the function ouside the loop it works, if i call it inside the for loop no plots are shown. Maybe you can help me on this problem?

[cderv]

When using for loop in knitr you may need to call print explicitly on the object.

See example with table in 10.1 The function knitr::kable() | R Markdown Cookbook

Otherwise, you can use knit_child to iterate on a list and produce output to include in the document

14.7 Use knitr::knit_expand() to generate Rmd source | R Markdown Cookbook

[weldbild]

Thank you for the hint with knit_child I finally managed to plot it. Even though I dont really know what you mean with the print(), because as you see in my code i already use print() inside the for loop ?

[cderv]

Oh I missed that. It means the basic print is not enough and probably a knit_print method comes into play.

With knitr printing object to be included into output document must sometimes be different that usual print.
Custom Print Methods

By using knit_child you ensure that the correct knitr tools are run correctly for the printing.