setwd("/var/www/forge2/production/src/html/files/0x454A546E8E9C11EA8198793F5BFE3F98")
results<-read.table("Unnamed.GWAS.erc.chart.tsv.gz", header = TRUE, sep="\t")

# Class splits the data into non-significant, marginally significant and significant according to 0.05 and 0.01 (in -log10 scale)
results$Class <- cut(results$Pvalue, breaks =c(0, 0.01, 0.05, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE)

# Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted)
results$Class2 <- cut(results$Qvalue, breaks =c(0, 0.01, 0.05, 1), labels=FALSE, include.lowest=TRUE)

color.axis.palette = c();
if (length(which(results$Class2 == 1)) > 0 ) {
    color.axis.palette = c('red');
}
if (length(which(results$Class2 == 2)) > 0 ) {
    color.axis.palette = c(color.axis.palette, '#FF82ab');
}
color.axis.palette = c(color.axis.palette, 'lightblue');
if (length(color.axis.palette) <= 2) {
    color.axis.palette = c(color.axis.palette, 'lightblue'); # Add it twice to force the color if only non-significant values
}

results$log10pvalue <- -log10(results$Pvalue)

# Re-order the entries according to tissue first and then cell type/line
tissue.cell.order <- unique(results[, c('Tissue', 'Cell')])
tissue.cell.order <- tissue.cell.order[order(tissue.cell.order[,1], tissue.cell.order[,2]), ]
# Collapse into a single string (to support same cell type in different tissues)
tissue.cell.order2 <- apply(tissue.cell.order, 1, paste, collapse = ' -- ')
results$TissueCell <- apply(results[, c('Tissue', 'Cell')], 1, paste, collapse = ' -- ')
results$TissueCell <- factor(results$TissueCell, levels=tissue.cell.order2)

# Count number of cell types for each tissue (to be able to draw the vertical separation lines afterwards
tissues <- c(0, cumsum(summary(tissue.cell.order[,'Tissue'])))

require(rCharts)

dplot.height=900
dplot.width=2000
bounds.x=60
bounds.y=50
bounds.height=dplot.height - 300
bounds.width=dplot.width - bounds.x - 20

# Create a dimple plot, showing p-value vs cell, split data by tissue, cell, probe, etc to see individual points instead of aggregate avg
d1 <- dPlot(
  y = 'log10pvalue',
  x = c('TissueCell'),
  groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Datatype', 'Probe', 'Class2'),
  data = results,
  type = 'bubble',
  width = dplot.width,
  height = dplot.height,
  bounds = list(x=bounds.x, y=bounds.y, height=bounds.height, width=bounds.width),
  id = 'chart.Unnamed.GWAS.erc'
)

# Force the order on the X-axis
d1$xAxis( type = 'addCategoryAxis', grouporderRule = 'Cell',       orderRule = tissue.cell.order[,2])
d1$xAxis( type = 'addCategoryAxis', grouporderRule = 'TissueCell', orderRule = as.factor(tissue.cell.order2))

d1$yAxis( type = 'addMeasureAxis' )

# Color points according to the q-value

d1$colorAxis(
   type = 'addColorAxis',
   colorSeries = 'Class2',
   palette = color.axis.palette)

# Builds a JS string to add labels for tissues
labels.string = paste(paste0("
    // Adds labels for tissues
    myChart.svg.insert('text', 'g')
      .attr('x', 0)
      .attr('y', 0)
      .attr('font-size', 16)
      .attr('font-family', 'Arial')
      .style('fill', '#A9A9A9')
      .attr('transform', 'translate(", (bounds.x + 5 + bounds.width * (tissues[1:(length(tissues)-1)] +  tissues[2:length(tissues)]) / (2 * max(tissues))), ", 60) rotate(-90)')
      .attr('text-anchor', 'end')
      .text('", names(tissues[2:length(tissues)]), "')
"), collapse='')

# Builds a JS string to add vertical lines to separate tissues
lines.string = paste(paste0("
    // Adds vertical lines between tissues
    myChart.svg.append('line')
      .attr('x1', ", (bounds.x + bounds.width * tissues[2:(length(tissues)-1)]/ max(tissues)), ")
      .attr('y1', 50)
      .attr('x2', ", (bounds.x + bounds.width * tissues[2:(length(tissues)-1)]/ max(tissues)), ")
      .attr('y2', ", (50 + bounds.height), ")
      .style('stroke', '#A9A9A9')
      .style('stroke-dasharray', '10,3,3,3')
"), collapse='')

# Adds some JS to be run after building the plot to get the image we want
d1$setTemplate(afterScript = paste0("
  <script>
    myChart.draw()
    
    myChart.svg
      .selectAll('.dimple-bubble')
      .filter(function(d) { return (d['aggField'][3] < 0.01); })
      .style('fill', function(d) {
        var datatype = d['aggField'][4];
        // http://pinetools.com/darken-color to darken hex values for chromatin states
        switch (datatype) {
          case 'H3K27me3':
            return '#e5e500';
          case 'H3K4me1':
            return '#e41a1c';
          case 'H3K4me3':
            return '#4daf4a';
          case 'H3K36me3':
            return '#984ea3';
          case 'H3K9me3':
            return '#ff7f00';
          case 'TssA':
            return '#FF0000';
          case 'TssAFlnk':
            return '#FF4500';
          case 'TxFlnk':
            return '#32CD32';
          case 'Tx':
            return '#008000';
          case 'TxWk':
            return '#006400';
          case 'EnhG':
            return '#C2E105';
          case 'Enh':
            return '#E5E500';
          case 'ZNF-Rpts':
            return '#3D7B66';
          case 'Het':
            return '#8A91D0';
          case 'TssBiv':
            return '#CD5C5C';
          case 'BivFlnk':
            return '#E9967A';
          case 'EnhBiv':
            return '#BDB76B';
          case 'ReprPC':
            return '#808080';
          case 'ReprPCWk':
            return '#C0C0C0';
          case 'Quies':
            return '#F8F8F8';
          default:
            return '#ff0000';
        }
      })
      .style('stroke', function(d) {
        var datatype = d['aggField'][4];
        switch (datatype) {
          case 'H3K27me3':
            return '#e5e500';
          case 'H3K4me1':
            return '#e41a1c';
          case 'H3K4me3':
            return '#4daf4a';
          case 'H3K36me3':
            return '#984ea3';
          case 'H3K9me3':
            return '#ff7f00';
          case 'TssA':
            return '#7f0000';
          case 'TssAFlnk':
            return '#7f2200';
          case 'TxFlnk':
            return '#186618';
          case 'Tx':
            return '#004000';
          case 'TxWk':
            return '#006400';
          case 'EnhG':
            return '#003200';
          case 'Enh':
            return '#727200';
          case 'ZNF-Rpts':
            return '#1e3d32';
          case 'Het':
            return '#31387b';
          case 'TssBiv':
            return '#712222';
          case 'BivFlnk':
            return '#983919';
          case 'EnhBiv':
            return '#66622d';
          case 'ReprPC':
            return '#404040';
          case 'ReprPCWk':
            return '#606060';
          case 'Quies':
            return '#7c7c7c';
          default:
            return '#ff0000';
        }
      });
      
    myChart.svg
      .selectAll('.dimple-bubble')
      .filter(function(d) { return ((d['aggField'][3] >= 0.01) && (d['aggField'][3] < 0.05)); })
      .style('stroke', function(d) {
        var datatype = d['aggField'][4];
        switch (datatype) {
          case 'H3K27me3':
            return '#e5e500';
          case 'H3K4me1':
            return '#e41a1c';
          case 'H3K4me3':
            return '#4daf4a';
          case 'H3K36me3':
            return '#984ea3';
          case 'H3K9me3':
            return '#ff7f00';
          case 'TssA':
            return '#FF0000';
          case 'TssAFlnk':
            return '#FF4500';
          case 'TxFlnk':
            return '#32CD32';
          case 'Tx':
            return '#008000';
          case 'TxWk':
            return '#006400';
          case 'EnhG':
            return '#C2E105';
          case 'Enh':
            return '#E5E500';
          case 'ZNF-Rpts':
            return '#3D7B66';
          case 'Het':
            return '#8A91D0';
          case 'TssBiv':
            return '#CD5C5C';
          case 'BivFlnk':
            return '#E9967A';
          case 'EnhBiv':
            return '#BDB76B';
          case 'ReprPC':
            return '#808080';
          case 'ReprPCWk':
            return '#C0C0C0';
          case 'Quies':
            return '#F8F8F8';
          default:
            return '#FF82ab';
        }
      })
      .style('stroke-width', '2')
      .style('fill', 'white');
      
    myChart.svg
      .selectAll('.dimple-bubble')
      .filter(function(d) { return (d['aggField'][3] >= 0.05); })
      .style('stroke', 'rgb(173, 216, 230)')
      .style('fill', 'white');

    // Substitutes TissueCell labels in X-axis by Cell labels
    myChart.axes[1].shapes
      .selectAll('text')
      .text(function (d) { 
           var i;
           for (i = 0; i < data.length; i += 1) {
               if (data[i].TissueCell === d) {
                   return data[i].Cell;
               }
           }
      })
      .style('text-anchor', 'start');

//       .attr('transform', function() {
//         var t = d3.transform(d3.select(this).attr('transform'));
//         return 'rotate(-90) translate(' + -1*parseFloat(t.translate[0]) + ', ' + -0.7*parseFloat(t.translate[1]) + ')';
//       });

    // Adds title for X-axis
    myChart.axes[1].titleShape
        .style('font-size', 20)

    // Adds title for Y-axis
    myChart.axes[2].titleShape
        .style('font-size', 20)
        .text('-log10 binomial p-value')

    // Adds main title
    myChart.svg.append('text')
      .attr('x', ", (dplot.width / 2), ")
      .attr('y', ", (bounds.y / 2), ")
      .attr('font-size', 24)
      .attr('font-family', 'Arial')
      .attr('font-weight', 'bold')
      .style('fill', 'black')
      .attr('text-anchor', 'middle')
      .text('DMPs in DNase I sites (probably TF sites) in cell lines for erc Unnamed')
    ", labels.string, "
    ", lines.string, "
    // Adds vertical line at the far right of the plot
    myChart.svg.append('line')
      .attr('x1', ", (bounds.x + bounds.width), ")
      .attr('y1', ", bounds.y, ")
      .attr('x2', ", (bounds.x + bounds.width), ")
      .attr('y2', ", (bounds.y + bounds.height), ")
      .style('stroke', 'rgb(0,0,0)')
  </script>
"))


d1$save('Unnamed.GWAS.erc.dchart.html', cdn = F)