report.Rmd

---
title: "Perturbation Analysis Report"
output: html_document
params:
  perturbationCounter: NA
  graphHistory: !r list()
  pvHistory: !r list()
  peHistory: !r list()
  delEventHistory: !r list()
 
---

```{r eval = FALSE, echo = FALSE}
# For PDF output, change the header to have "output: pdf_document".
#
# Note that due to an issue in rmarkdown, the default value of a parameter in
# the header cannot be `NULL`, so I used a default of `NA` for the default value
# of `n`.
require(igraph)
require(knitr)
require(xtable)
```



```{r results= 'asis', echo = FALSE}

# https://stackoverflow.com/questions/28313600/r-knitr-print-in-a-loop
# https://github.com/yihui/knitr/issues/886


#https://stackoverflow.com/questions/32418860/output-markdown-in-r-code-chunk
for (i in 1:params$perturbationCounter){
  
  cat('\n')
  
  cat(paste0("### ",params$delEventHistory[[i]]))
  
  cat('\n')
  
  coords <- layout_(params$graphHistory[[i]], as_star())
  
  plot(params$graphHistory[[i]], layout = coords, edge.arrow.size = 0.4,
     vertex.size = 25, vertex.label.family = "Arial Black")

  cat('\n')
  
  print(knitr::kable(params$pvHistory[[i]], caption = "Possible node perturbations", 
             row.names = FALSE))
   cat('\n')

  print(knitr::kable(params$peHistory[[i]], caption = "Possible link perturbations", 
             row.names = FALSE))
  
   cat('\n')
  
  }
```