updated epimatrix chord2 color scheme

hetmanb · Nov 18, 2014 · 23efeff · 23efeff
1 parent ca54a85
commit 23efeff
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Showing 3 changed files with 29 additions and 12 deletions.
diff --git a/helpers/chord_helper.R b/helpers/chord_helper.R
@@ -37,6 +37,28 @@ chordcolor <- function(data, low, high){
   chord_table$color <- (colors)
 #   chord_table <- subset(chord_table, subset = (chord_table$count >= low) & (chord_table$count <= high) )
 
+  palette <- as.vector(as.character(chord_table$color))
+  return(palette)
+}  
+chord2color <- function(data, low, high){
+
+  chord_table <- data
+  colnames(chord_table) <- c("has", "prefers", "count")
+  chord_table <- unique(chord_table)
+  chord_table <- subset(chord_table, subset = (chord_table$count >= low) & (chord_table$count <= high) )
+
+
+  values <- chord_table$count
+
+
+  ii <- cut(values, breaks = seq(min(values), max(values), len = length(values)), 
+            include.lowest = TRUE)
+
+  colors <- colorRampPalette(c("#F7FCF5","#E5F5E0","#C7E9C0","#A1D99B","#74C476","#41AB5D","#238B45","#005A32"))(length(ii))[ii]
+
+  chord_table$color <- (colors)
+  #   chord_table <- subset(chord_table, subset = (chord_table$count >= low) & (chord_table$count <= high) )
+
   palette <- as.vector(as.character(chord_table$color))
   return(palette)
 }  
diff --git a/server.R b/server.R
@@ -168,18 +168,10 @@ shinyServer(function(input, output, session) {
      if(is.null(input$strain_data)) { inFile <- read.table('data/demo_data/demo_58_strainlist.txt', header=T, sep='\t')  }     
       else { inFile <- read.table(input$strain_data$datapath, header=T, sep='\t') } 
        return(EpiMap(inFile))
-
-# #     inFile <- read.table(file = 'data/strain_data.txt' , header = T)
-# #     markerlist <- list(c(inFile$Latitude, inFile$Longitude)) 
-#     epimap <- Leaflet$new()
-#     epimap$setView(c(49.6942, -112.8328), zoom = 6)
-# #     epimap$marker <- markerlist
-#     #epimap$marker(c(51.5, -0.09), bindPopup = "<p> Hi. I am a popup </p>")
-#     #epimap$marker(c(51.495, -0.083), bindPopup = "<p> Hi. I am another popup </p>")
-#     epimap
+
    })
 
-############ Functions for the Source Chord Diagram JS Output: #############################
+############ Functions for the Epi-Chord Diagram JS Output: #############################
 
 chord2_in <- reactive({ 
   melt(EpiMatrix(table()))
@@ -188,12 +180,15 @@ chord2_in <- reactive({
 chord2_file <- reactive({
   chord_table(chord2_in(), input$chord2_low, input$chord2_high)
 })
+chord2_color <- reactive({
+  chord2color(chord2_in(), input$chord2_low, input$chord2_high)
+})
 
 output$jschord2 <- reactive({
   # List of arguments given to the chord.js file     
   list(
     filepath = as.matrix(chord2_file()), 
-    color = brewer.pal(n = 8, name = "Greens") 
+    color = chord2_color() 
   )
 })
 

diff --git a/ui.R b/ui.R
@@ -148,7 +148,7 @@ shinyUI(navbarPage(theme = "united.css",
                                            shiny_alert_container('epi_chord_alert'),
                                            br(), 
                                            #shiny_alert_container('source_chord_alert'),
-                                           sliderInput("chord2_low", "Low Threshold for Similarity", min=0, max=1.0, value=0.9, step=0.01), 
+                                           sliderInput("chord2_low", "Low Threshold for Similarity", min=0, max=1.0, value=0.7, step=0.01), 
                                            sliderInput("chord2_high", "High Threshold for Similarity", min=0, max=1.0, value=.95, step=0.01),
                                            br(),
                                            busyIndicator("Processing...", wait = 500),