CI-LM/Ci-matrix-render.R

In lrutter/RNASeqVisualization:

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

ui <- shinyUI(fluidPage(
  sliderInput("ci", "Confidence interval:", min = 0, max = 1, 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=rnorm(100), A.2=rnorm(100), A.3=rnorm(100), B.1=rnorm(100), B.2=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)

#st = qt(1-(1-0.999)/2,(nrow(dat)-2))
#st = 150

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) {

     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);
     }

     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)

       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;
         sea = data.sse[j] * Math.sqrt(1/n+Math.pow((a-xm),2)/ssx);
         yv.push(yva);
         se.push(sea);
         ci.push(data.st*sea);
         uyv.push(yva+data.st*sea);
         lyv.push(yva-data.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]]
         ssea.push(data.sse[j] * Math.sqrt(1/n+Math.pow((xa-xm),2)/ssx))
         ypred.push(data.b0[j]+data.b1[j]*xa)
         lwr.push(ypred[a] - ssea[a]*data.st)
         upr.push(ypred[a] + ssea[a]*data.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=ci())))})

shinyApp(ui, server)