logical merge

data/maxKnownKs.csv

@@ -1,2 +1,2 @@
 "","K.2","K.4","K.5","K.6","K.9"
-"1",39.0641988031379,40.5065171208468,42.2639233189173,43.6574062551325,52.8978703506378
+"1",37.0641988031379,40.5065171208468,42.2639233189173,43.6574062551325,52.8978703506378

report.Rmd

@@ -2,9 +2,12 @@
 title: "Perturbation Analysis Report"
 output: html_document
 params:
-  g: NA #default value 
-  pv: NA
-  pe: NA
+  perturbationCounter: NA
+  graphHistory: !r list()
+  pvHistory: !r list()
+  peHistory: !r list()
+  delEventHistory: !r list()
+
 ---
 
 ```{r eval = FALSE, echo = FALSE}
@@ -15,20 +18,42 @@ params:
 # of `n`.
 require(igraph)
 require(knitr)
+require(xtable)
 ```
 
-```{r echo = FALSE}
 
-coords <- layout_(params$g, as_star())
 
-plot(params$g, 
-     layout = coords, edge.arrow.size = 0.4,
-     vertex.size = 25, vertex.label.family = "Arial Black")
+```{r results= 'asis', echo = FALSE}
+
+# https://stackoverflow.com/questions/28313600/r-knitr-print-in-a-loop
+# https://github.com/yihui/knitr/issues/886
 
 
-knitr::kable(params$pv, caption = "Vertex perturbations", 
-             row.names = FALSE) 
+#https://stackoverflow.com/questions/32418860/output-markdown-in-r-code-chunk
+for (i in 1:params$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")
 
-knitr::kable(params$pe, caption ="Edge perturbations")
+  cat('\n')
+
+  print(knitr::kable(params$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')
+
+  }
+```
 
-```

server.R

@@ -410,13 +410,21 @@ shinyServer(function(input, output, session) {
 
   sizeOfHistory <- vcount(g) + ecount(g)
 
-  graphHistory    <- vector("list", sizeOfHistory)
-  ptHistory       <- vector("list", sizeOfHistory)
-  pvHistory       <- vector("list", sizeOfHistory)
-  peHistory       <- vector("list", sizeOfHistory)
+  graphHistory    <- list()
+
+  pvHistory       <- list()
+
+  peHistory       <- list()
+
   delEventHistory <- vector("list", sizeOfHistory)
 
-  perturbationCounter <- as.integer(0)
+  graphHistory[[1]]    <- g
+  pvHistory[[1]]       <- relabelVertexTable(pv)
+  peHistory[[1]]       <- relabelEdgeTable(pe)
+  delEventHistory[[1]] <- "Initial state of the network"
+
+  #starts with 1 even though the network hasn't been changed at the start
+  perturbationCounter <- as.integer(1)
 
   my <- reactiveValues(g = g,
                        pv = pv,
@@ -445,15 +453,18 @@ shinyServer(function(input, output, session) {
     if (is.null(inFile$datapath)){
 
 
-
     } else {
 
-      g <- loadGraph(inFile$datapath)
+      g <- loadGraphPA(inFile$datapath)
       my$pv <- calculatePerturbationByVertexDeletion(g, 4, 1)
       my$pe <- calculatePerturbationByEdgeDeletion(g, 4, 1)
       my$g  <- setGraphColors(g, my$pv, my$pe)
 
       my$sizeOfHistory <- vcount(my$g) + ecount(my$g)
+
+      my$perturbationCounter <- as.integer(1)
+
+      #todo: check if this vector("list", my$sizeOfHistory) works with list() in Report.Rmd
       graphHistory     <- vector("list", my$sizeOfHistory)
       ptHistory        <- vector("list", my$sizeOfHistory)
       pvHistory        <- vector("list", my$sizeOfHistory)
@@ -469,12 +480,26 @@ shinyServer(function(input, output, session) {
 
     if(vcount(my$g) > 5){
 
+      my$perturbationCounter <- my$perturbationCounter + 1
+
+
+
       my$g <- delete_vertices(my$g,
                               input$vertexToDelete)
 
       my$pv <- calculatePerturbationByVertexDeletion(my$g, 4, 1)
       my$pe <- calculatePerturbationByEdgeDeletion(my$g, 4, 1)
 
+      my$g  <- setGraphColors(my$g, my$pv, my$pe)
+
+      my$graphHistory[[my$perturbationCounter]] <- my$g
+      my$pvHistory[[my$perturbationCounter]]    <- relabelVertexTable(my$pv)
+      my$peHistory[[my$perturbationCounter]]    <- relabelEdgeTable(my$pe)
+
+      my$delEventHistory[[my$perturbationCounter]] <- paste0("Deletion of node ", 
+                                                             input$vertexToDelete)    
+
+
     }
 
     else {
@@ -499,6 +524,18 @@ shinyServer(function(input, output, session) {
       my$pv <- calculatePerturbationByVertexDeletion(my$g, 4, 1)
       my$pe <- calculatePerturbationByEdgeDeletion(my$g, 4, 1)
 
+      my$g  <- setGraphColors(my$g, my$pv, my$pe)
+
+      my$perturbationCounter <- my$perturbationCounter + 1
+
+      my$graphHistory[[my$perturbationCounter]] <- my$g
+      my$pvHistory[[my$perturbationCounter]]    <- relabelVertexTable(my$pv)
+      my$peHistory[[my$perturbationCounter]]    <- relabelEdgeTable(my$pe)
+
+
+      my$delEventHistory[[my$perturbationCounter]] <- paste0("Deletion of link ", 
+                                                             input$edgeToDelete) 
+
     } else {
 
       output$cantDeleteLink <- renderText("can't delete more links")
@@ -557,9 +594,11 @@ shinyServer(function(input, output, session) {
       printET <- relabelEdgeTable(my$pe)
 
 
-      params <- list(g = printG,
-                     pv = printVT,
-                     pe = printET)
+      params <- list(graphHistory = my$graphHistory,
+                     pvHistory = my$pvHistory,
+                     peHistory = my$peHistory,
+                     perturbationCounter = my$perturbationCounter,
+                     delEventHistory = my$delEventHistory)
 
       rmarkdown::render(tempReport, 
                         output_file = file,