diff --git a/jass/static/chromo_heatmap_manhattan_by_region.html b/jass/static/chromo_heatmap_manhattan_by_region.html
index 0eeab83076be0d90d1b7bf70c603b1fb96645875..84d1060b0d0c7ba9a3e35bd62fa9cd8be0f6798d 100644
--- a/jass/static/chromo_heatmap_manhattan_by_region.html
+++ b/jass/static/chromo_heatmap_manhattan_by_region.html
@@ -108,6 +108,7 @@
<select id="HeatList" onChange="redrawHeatmap()" hidden="true"></select>
<div id="exportHeatPlot" hidden="true"><button id="exportHeatmap" >Export</button></div>
<div id="divLocalStatPlot" ><!-- Plotly chart will be drawn inside this DIV --></div>
+ <div id="myDiv"></div>
<script>
@@ -192,12 +193,23 @@
});
heatColors.appendChild(fragmentHeat);
-
+
$('#summaryStat').show();
-
- selectRegion();
- $('#HeatList').show();
+ $.get("/api/projects/" + idProject + "/dispo_gene_exon", function( data1 ) {
+ console.log("dispo_gene_exon="+data1);
+ if (data1 == "READY"){
+ gene_and_exon();
+ }
+ else {
+ $.get("/api/projects/" + idProject + "/error_msg", function( data2 ) {
+ var User_Message3 = "An error has occurred: please check your data \n " + data2;
+ alert(User_Message3);
+ });
+ }
+ selectRegion();
+ $('#HeatList').show();
+ });
console.log("Sortie de la fonction init() " ); //__Modif__CN__
}
@@ -354,7 +366,7 @@
{
x: [d, e],
y: [genomelocalline, genomelocalline],
- mode: 'lines+markers+text',
+ mode: 'lines',
name: 'significance treshold',
textposition: 'top',
type: 'scatter',
@@ -885,6 +897,302 @@
// ---------------------------------------------------------------------------------------------------------------------------
+ function create_the_graph_of_genes_and_exons(GeneID,
+ gene_label,
+ gene_start,
+ gene_end,
+ gene_direction,
+ gene_biotype,
+ exons,
+ start,
+ end){
+ var NB_lines = 3;
+ var left_arrow = "\u2190 ";
+ var right_arrow = " \u2192";
+ var y_coord = [14.5, 11.5, 8.5, 5.5, 2.5];
+ const K_PROTEIN_CODING = 0;
+ const K_rRNA = 1;
+ const K_OTHER = 2;
+ var color_gene = ["rgb(0, 0, 111)",
+ "rgb(120, 0, 0)",
+ "rgb(0, 120, 0)"];
+ var color_exon = ["rgb(0, 0, 255)",
+ "rgb(255, 0, 0)",
+ "rgb(0, 180, 0)"];
+
+ var k = -1;
+ var genes_and_exons_shapes = new Array();
+ var genes_x = new Array();
+ var genes_y = new Array();
+ var the_genes_label = new Array();
+ for (i = 0; i < 3; i++) {
+ var genes_x_i = new Array();
+ genes_x.push(genes_x_i);
+ var genes_y_i = new Array();
+ genes_y.push(genes_y_i);
+ var the_genes_label_i = new Array();
+ the_genes_label.push(the_genes_label_i);
+ }
+ var data = new Array();
+ var label_biotype = ["protein coding", "rRNA", "other"];
+ var label_exon = ["coding gene", "gene rRNA", "other gene"];
+
+ for (i = 0; i < GeneID.length; i++) {
+ k = k + 1;
+ if (k >= NB_lines) {k = 0;}
+
+ var coord_x = (gene_start[i] + gene_end[i]) / 2;
+ var coord_y = y_coord[k] + 1;
+ if (gene_direction[i] == "-") {
+ var the_label = left_arrow + gene_label[i];
+ }
+ else {
+ var the_label = gene_label[i] + right_arrow;
+ }
+
+ if (gene_biotype[i] == "protein_coding") {
+ color_number = K_PROTEIN_CODING;
+ }
+ else if (gene_biotype[i] == "rRNA") {
+ color_number = K_rRNA;
+ }
+ else {
+ color_number = K_OTHER;
+ }
+
+ genes_x[color_number].push(coord_x);
+ genes_y[color_number].push(coord_y);
+ the_genes_label[color_number].push(the_label);
+
+ var nouveau_gene = {
+ type: 'line',
+ x0: gene_start[i],
+ y0: y_coord[k],
+ x1: gene_end[i],
+ y1: y_coord[k],
+ line: {
+ color: color_gene[color_number],
+ width: 3
+ }
+ };
+
+ exon_data = exons.get(GeneID[i]);
+ exon_label = exon_data.label;
+ exon_start = exon_data.start;
+ exon_end = exon_data.end;
+
+ for (j = 0; j < exon_label.length; j++) {
+ var nouvel_exon = {
+ type: 'rect',
+ x0: exon_start[j],
+ y0: y_coord[k] - 0.5,
+ x1: exon_end[j],
+ y1: y_coord[k] + 0.5,
+ line: {
+ color: color_exon[color_number],
+ width: 1
+ },
+ fillcolor: color_exon[color_number]
+ };
+ genes_and_exons_shapes.push(nouvel_exon);
+ }
+
+ genes_and_exons_shapes.push(nouveau_gene);
+ }
+
+ var legend_group = ["GENES", "EXONS"];
+ for (i = 0; i < 2; i++) {
+ var tip_group_legend_title = {
+ mode: 'lines',
+ type: 'scatter',
+ x: [gene_start[0],gene_end[0]],
+ y: [y_coord[0], y_coord[0]],
+ legendgroup: legend_group[i],
+ line: {
+ width: 0,
+ color: 'white'
+ },
+ name: legend_group[i],
+ showlegend: true,
+ };
+ data.push(tip_group_legend_title);
+ }
+
+ for (i = 0; i < 3; i++) {
+ if (genes_x[i].length > 0) {
+ var label_genes = {
+ x: genes_x[i],
+ y: genes_y[i],
+ text: the_genes_label[i],
+ mode: 'text',
+ textfont: {
+ family: "Calibri, Arial, Times New Roman",
+ size: 14,
+ color: color_gene[i]
+ },
+ showlegend: false,
+ };
+
+ data.push(label_genes);
+
+ var tip_legend = {
+ mode: 'lines',
+ type: 'scatter',
+ x: [gene_start[0],gene_end[0]],
+ y: [y_coord[0], y_coord[0]],
+ legendgroup: legend_group[0],
+ line: {
+ color: color_gene[i],
+ width: 3
+ },
+ name: label_biotype[i],
+ showlegend: true,
+ };
+ data.push(tip_legend);
+ var tip_legend = {
+ mode: 'lines',
+ type: 'scatter',
+ x: [gene_start[0],gene_end[0]],
+ y: [y_coord[0], y_coord[0]],
+ legendgroup: legend_group[1],
+ line: {
+ color: color_exon[i],
+ width: 1
+ },
+ name: label_exon[i],
+ showlegend: true,
+ };
+ data.push(tip_legend);
+ }
+ }
+
+ var margin_axis = Math.ceil((end - start)/20);
+ var new_start = start - margin_axis;
+ var new_end = end + margin_axis;
+ var layout = {
+ title: 'Genes and exons',
+ showlegend: true ,
+ legend: {
+ title: {
+ text: 'Biotype of the genes'
+ },
+ font: {
+ size: 8
+ },
+ },
+ margin: {
+ l: 95,
+ r: 50,
+ b: 60,
+ t: 100,
+ pad: 4
+ },
+ xaxis: {
+ range: [new_start, new_end],
+ title: "position",
+ titlefont: {
+ size: 10
+ },
+ tickmode: 'auto',
+ tickfont: {
+ size: 10
+ },
+ nticks: 20
+ },
+ yaxis: {
+ range: [0, 20],
+ autotick: true,
+ ticks: '',
+ showticklabels: false ,
+ showgrid: false
+ },
+ width: plotSize,
+ height: 500,
+ shapes: genes_and_exons_shapes
+ };
+
+ Plotly.newPlot('myDiv', data, layout);
+ }
+
+// ---------------------------------------------------------------------------------------------------------------------------
+
+ function gene_and_exon(){
+
+ console.log("Entrée dans la fonction gene_and_exon " ); //__Modif__CN__
+
+ console.log("/api/projects/"+idProject+"/gene_exon");
+ Plotly.d3.csv("/api/projects/" + idProject + "/gene_exon",
+ function(data){ process_gene_and_exon(data) } );
+
+ console.log("Sortie de la fonction gene_and_exon" ); //__Modif__CN__
+
+ }
+
+
+// ---------------------------------------------------------------------------------------------------------------------------
+
+ function process_gene_and_exon(rows) {
+
+ console.log("Entrée dans la fonction process_gene_and_exon(rows) " ); //__Modif__CN__
+
+ var start = parseInt(sessionStorage.getItem("start"));
+ var end = parseInt(sessionStorage.getItem("end"));
+
+ console.log("rows.length "+rows.length);
+ var GeneID = new Array();
+ var gene_label = new Array();
+ var gene_start = new Array();
+ var gene_end = new Array();
+ var gene_direction = new Array();
+ var gene_biotype = new Array() ;
+ var exons = new Map();
+
+ var Gene__ID_old = new Array();
+ Gene__ID_old.push("");
+
+ for (var i = 0 ; i < rows.length ; i++) {
+ var ligne = rows[i];
+ var Gene__ID = ligne.GeneID;
+ if (Gene__ID_old.includes(Gene__ID) == false) {
+ Gene__ID_old.push(Gene__ID);
+ GeneID.push(Gene__ID);
+ var Gene__label = ligne.gene_label;
+ gene_label.push(Gene__label);
+ var Gene__start = Math.max(parseInt(ligne.gene_start), start);
+ gene_start.push(Gene__start);
+ var Gene__end = Math.min(parseInt(ligne.gene_end), end);
+ gene_end.push(Gene__end);
+ var Gene__direction = ligne.gene_direction;
+ gene_direction.push(Gene__direction);
+ var Gene__biotype = ligne.gene_biotype;
+ gene_biotype.push(Gene__biotype);
+
+ var Exon__label = new Array();
+ var Exon__start = new Array();
+ var Exon__end = new Array();
+ exons.set(Gene__ID, {
+ label: Exon__label,
+ start: Exon__start,
+ end: Exon__end});
+ }
+ exon_data = exons.get(Gene__ID);
+ exon_data.label.push(ligne.exon_label);
+ exon_data.start.push(parseInt(ligne.exon_start));
+ exon_data.end.push(parseInt(ligne.exon_end));
+
+ }
+
+ create_the_graph_of_genes_and_exons(GeneID,
+ gene_label,
+ gene_start,
+ gene_end,
+ gene_direction,
+ gene_biotype,
+ exons,
+ start,
+ end);
+ }
+
</script>
</body>