CI-LM/Pi-matrix-render.R

In lrutter/RNASeqVisualization:

library(plotly)
library(htmlwidgets)
library(shiny)
library(GGally)

ui <- shinyUI(fluidPage(
  sliderInput("ci", "Prediction interval:", min = 0, max = 0.99, value=0.95, step=0.01),
  plotlyOutput("myPlot")
))

server <- shinyServer(function(input, output) {

  ci <- reactive(input$ci)

  set.seed(2)
  dat <- data.frame(ID = paste0("ID",1:100), A.1=sort(rnorm(100)), A.2=sort(rnorm(100)), A.3=sort(rnorm(100)), B.1=sort(rnorm(100)), B.2=sort(rnorm(100)))

  #load("../leavesDat.Rda")
  #dat <- data.frame(ID = paste0("ID",1:nrow(data)), M.1=data[,2], M.2=data[,3], M.3=data[,4], P.1=data[,5], P.2=data[,6], P.3=data[,7])
  #dat <- dat[1:100,]

  dat$ID <- as.character(dat$ID)
  nCol = ncol(dat)

  conf=seq(0,0.99,.01)
  st<- qt(1-(1-conf)/2,(nrow(dat)-2))

  b0 = c()
  b1 = c()
  sse = c()
  for (i in 2:(nCol-1)){
    j = nCol
    while (j >i){
      datXY <- as.data.frame(cbind(x = dat[,i], y = dat[,j]))
      datLm <- lm(y~x,data=datXY)
      b0 <- c(b0, coef(datLm)[1])
      b1 <- c(b1, coef(datLm)[2])
      sse <- c(sse, summary(datLm)[[6]])
      j = j-1
    }
  }
  b0<-as.vector(b0)
  b1<-as.vector(b1)
  sse<-as.vector(sse)

  minVal = 0
  maxVal = max(dat[,-1])

  my_fn <- function(data, mapping, ...){
    x = data[,c(as.character(mapping$x))]
    y = data[,c(as.character(mapping$y))]
    p <- ggplot(data = dat, aes(x=x, y=y)) + coord_cartesian(xlim = c(minVal, maxVal), ylim = c(minVal, maxVal))
    p
  }

  p <- ggpairs(dat[,-1], lower = list(continuous = my_fn))

  ggPS <- ggplotly(p)

  myLength <- length(ggPS[["x"]][["data"]])
  for (i in 1:myLength){
    item =ggPS[["x"]][["data"]][[i]]$text[1]
    if (!is.null(item))
      if (!startsWith(item, "co")){
        ggPS[["x"]][["data"]][[i]]$hoverinfo <- "none"
      }
  }



  output$myPlot <- renderPlotly(ggPS %>%
  onRender("
   function(el, x, data) {

             function range(start, stop, step){
             var a=[start], b=start;
             while(b<stop){b+=step;a.push(b)}
             return a;
             };

   console.log('Start')
   len = Math.sqrt(document.getElementsByClassName('cartesianlayer')[0].childNodes.length);
   AxisNames = [];
   for (i = 1; i < (len+1); i++) {
   AxisNames.push(document.getElementsByClassName('infolayer')[0].childNodes[i].textContent);
   }

   stIndex = Math.round((1-0)/.01*data.ci)
   console.log(stIndex)
   st = data.st[stIndex]
   console.log(st)

   var Traces = [];
   var i=0;
   var j=0;
   var k=1;
   while ((i*len+k)<=Math.pow((len-1),2)) {
   while ((i+k)<len){
   var x = [];
   var y = [];
   var xTotal = 0;
   var ssx = 0;
   n = data.dat.length; // 100
   for (a=0; a<n; a++){
   xa = data.dat[a][AxisNames[i]]
   x.push(xa)
   y.push(data.dat[a][AxisNames[(len-k)]])
   xTotal+=xa
   }

   var xm = xTotal/n
   for (a=0; a<n; a++){
   ssx+=Math.pow((data.dat[a][AxisNames[i]] - xm),2)
   }

   var minX = Math.min.apply(null,x)
   var maxX = Math.max.apply(null,x)

   //console.log(x)
   //console.log(minX)
   //console.log(maxX)

   var inc = (maxX-minX)/100
   var xv = [];
   var yv = [];
   var se = [];
   var ci = [];
   var uyv = [];
   var lyv = [];
   var a = minX
   while (a < maxX){
   xv.push(a);
   yva = data.b0[j]+data.b1[j]*a;
   // just changed this to have 1+1/n instead of just 1/n
   sea = data.sse[j] * Math.sqrt(1+1/n+Math.pow((a-xm),2)/ssx);
   yv.push(yva);
   se.push(sea);
   ci.push(st*sea);
   uyv.push(yva+st*sea);
   lyv.push(yva-st*sea);
   a+=inc;
   }

   var lwr = [];
   var upr = [];
   var ypred = [];
   var ssea = [];
   var outCI = [];
   var xPoints = [];
   var yPoints = [];
   for (a=0; a<n; a++){
   xa = data.dat[a][AxisNames[i]]
   // just changed this to have 1+1/n instead of just 1/n
   ssea.push(data.sse[j] * Math.sqrt(1+1/n+Math.pow((xa-xm),2)/ssx))
   ypred.push(data.b0[j]+data.b1[j]*xa)
   lwr.push(ypred[a] - ssea[a]*st)
   upr.push(ypred[a] + ssea[a]*st)
   if (!(y[a]>lwr[a] & y[a]<upr[a])){
   xPoints.push(xa)
   yPoints.push(data.dat[a][AxisNames[(len-k)]])
   }
   }

   var tracePoints = {
   x: xPoints,
   y: yPoints,
   mode: 'markers',
   marker: {
   color: 'black',
   size: 2
   },
   xaxis: 'x' + (i+1),
   yaxis: 'y' + (i*len+k),
   hoverinfo: 'none'
   };
   var hiLine = {
   x: xv,
   y: uyv,
   mode: 'lines',
   line: {
   color: 'gray',
   width: 1
   },
   xaxis: 'x' + (i+1),
   yaxis: 'y' + (i*len+k),
   opacity: 0.25,
   hoverinfo: 'none'
   };
   var lowLine = {
   x: xv,
   y: lyv,
   mode: 'lines',
   fill: 'tonexty',
   line: {
   color: 'gray',
   width: 1
   },
   xaxis: 'x' + (i+1),
   yaxis: 'y' + (i*len+k),
   opacity: 0.25,
   hoverinfo: 'none'
   };
   Traces.push(tracePoints);
   Traces.push(hiLine);
   Traces.push(lowLine);
   j++;
   k++;
   }
   i++;
   k=1;
   }
   Plotly.addTraces(el.id, Traces);
   }
   ", data = list(dat=dat, b0=b0, b1=b1, sse=sse, st=st, ci=ci())))})

shinyApp(ui, server)