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d3 clustergram with zooming and searching
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| /* prevents horizontal scrolling */ | |
| html { | |
| /*min-width: 1040px;*/ | |
| max-width: 100%; | |
| overflow-x: hidden; | |
| } | |
| h1 { | |
| font-size: 45px; | |
| font-weight: 300; | |
| margin-top: 10px; | |
| margin-bottom: 20px; | |
| } | |
| h2 { | |
| margin-top: 2em; | |
| } | |
| /*grey background*/ | |
| .background { | |
| fill: #eee; | |
| } | |
| line { | |
| stroke: white; | |
| } | |
| text.active { | |
| font-weight: bold; | |
| } | |
| /*position the title of the columns and rows*/ | |
| #col_title{ | |
| font-size: 20px; | |
| display: block; | |
| margin-left:140px; | |
| margin-top:2px; | |
| font-weight: 300; | |
| } | |
| #row_title{ | |
| font-size:20px; | |
| display: block; | |
| transform:rotate(-90deg ); | |
| float:left; | |
| /*this is sensitive to the length of the | |
| row title*/ | |
| margin-left: -13px; | |
| margin-top: 300px; | |
| font-weight: 300; | |
| } | |
| #svg_div{ | |
| /*margin-top: 0px;*/ | |
| /*margin-left: 50px;*/ | |
| position:absolute; | |
| top:0px; | |
| left:25px; | |
| /*position:fixed;*/ | |
| /*float:left;*/ | |
| } | |
| #main_svg{ | |
| /*position:fixed;*/ | |
| /*top:100px; | |
| left:280px;*/ | |
| /*need to reduce this from -47px | |
| not sure why*/ | |
| margin-left: 0px; | |
| font-size:8.0px; | |
| display:inline-block; | |
| } | |
| /*try to get auto height*/ | |
| #wrapper{ | |
| height:100vh; | |
| } | |
| #main_container{ | |
| position: relative; | |
| margin-left: 30px; | |
| /*!! need to improve this*/ | |
| /*width:100%;*/ | |
| /*height:1000px;*/ | |
| } | |
| #initial_container{ | |
| position:relative; | |
| } | |
| #clust_and_row_container{ | |
| /*so that the child div can be positioned absolutely*/ | |
| position: relative; | |
| } | |
| /*the viz container is wider | |
| than the initial container | |
| because the sidebar will be closed*/ | |
| #viz_container{ | |
| position: relative; | |
| /*!! this constraints the width of svg*/ | |
| /*width: 80%;*/ | |
| /*background-color: blue;*/ | |
| } | |
| #clustergram_container{ | |
| display: block; | |
| border-style: solid; | |
| border-width: 3px; | |
| border-color: #f5f5f5; | |
| margin-top: 10px; | |
| /*set height here so that it will | |
| look normal with out clustergram*/ | |
| /*height: 950px;*/ | |
| margin-left: 260px; | |
| } | |
| #clust_instruct_container{ | |
| display: block; | |
| padding-left: 10px; | |
| border-left: 0px; | |
| /*border-style: solid;*/ | |
| /*border-width: 5px;*/ | |
| /*border-color: #f5f5f5;*/ | |
| /*set up fixed positions*/ | |
| position:absolute; | |
| width:245px; | |
| } | |
| #website_title{ | |
| margin-top: 20px; | |
| display: none; | |
| } | |
| #gene_input_box{ | |
| height:200px; | |
| width: 75%; | |
| margin: 0 auto; | |
| position:relative; | |
| display:block; | |
| resize:none; | |
| font-size: 15px; | |
| font-weight: 300; | |
| padding-left: 6px; | |
| } | |
| #title_input_gene_list{ | |
| width:99%; | |
| margin: 0 auto; | |
| color:white; | |
| text-align: center; | |
| margin-top: 32px; | |
| margin-bottom: 10px; | |
| font-size: 22px; | |
| font-weight: 300; | |
| } | |
| /*title for instructions*/ | |
| #title_viz_instruct_text{ | |
| width:99%; | |
| margin: 0 auto; | |
| color:#333; | |
| text-align: left; | |
| margin-top: 5px; | |
| padding-top:5px; | |
| margin-bottom: 5px; | |
| font-size: 22px; | |
| font-weight: 300; | |
| /*clear float left*/ | |
| clear:both; | |
| } | |
| /* the instructions for the visualization should | |
| look like the input gene list text title*/ | |
| .viz_instruct_text{ | |
| width:99%; | |
| margin: 0 auto; | |
| color:#333; | |
| text-align: left; | |
| margin-top:10px; | |
| margin-bottom: 10px; | |
| font-size: 14px; | |
| font-weight: 300; | |
| } | |
| .initial_paragraph{ | |
| font-size: 20px; | |
| width:590px; | |
| font-weight: 300; | |
| display: none; | |
| } | |
| #title_gmt_menu{ | |
| display: none; | |
| color:white; | |
| padding-top:12px; | |
| padding-bottom:12px; | |
| padding-left:20px; | |
| width:410px; | |
| text-align: left; | |
| background: #333333; | |
| font-size: 22px; | |
| font-weight: 300; | |
| } | |
| .h_top{ | |
| padding-left:20px; | |
| width:410px; | |
| text-align: left; | |
| background: #8C8C8C; | |
| font-size: 17px; | |
| font-weight: 300; | |
| border-radius: 0; | |
| opacity: 0; | |
| } | |
| .h_medium{ | |
| padding-left:30px; | |
| width:410px; | |
| text-align: left; | |
| background: #D0D0D0; | |
| border-radius: 0; | |
| font-size: 15px; | |
| font-weight: 300; | |
| padding-top: 0px; | |
| padding-bottom: 0px; | |
| } | |
| #gmt_menu{ | |
| display: none; | |
| margin-top: 20px; | |
| margin-left: 0px; | |
| font-size: 15px; | |
| font-weight: 300; | |
| } | |
| .buttons{ | |
| font-size: 15px; | |
| font-weight: 300; | |
| } | |
| .glyph_squares{ | |
| float: left; | |
| margin-right: 10px; | |
| margin-top: 0px; | |
| } | |
| #submit_genes_button{ | |
| width:141px; | |
| margin-bottom: 10px; | |
| } | |
| /*clear button*/ | |
| #clear_input_button{ | |
| opacity: 0.90; | |
| } | |
| /*return to previous enrichrgram button*/ | |
| #return_prev_button{ | |
| width: 140px; | |
| margin-top: 40px; | |
| opacity: 0.9; | |
| } | |
| /*modify enrichrgram*/ | |
| #modify_enrichrgram_button{ | |
| opacity: 1.0; | |
| } | |
| .form-group{ | |
| margin-bottom: 10px; | |
| } | |
| /*footer - shift it with the sidebar*/ | |
| #footer_div{ | |
| margin-left: 0px; | |
| } | |
| /*title for the visualization*/ | |
| #viz_website_title{ | |
| font-size: 33px; | |
| } | |
| /*container for gene search box*/ | |
| #gene_search_container{ | |
| margin-top: 10px; | |
| /*needed for some reason*/ | |
| margin-left: 0px; | |
| display: none:; | |
| } | |
| /*gene search box */ | |
| #gene_search_box{ | |
| width:120px; | |
| /*float:left;*/ | |
| /*display: none;*/ | |
| } | |
| /*gene search button*/ | |
| #gene_search_button{ | |
| /*width:50px;*/ | |
| /*float:left;*/ | |
| margin-top:-2px; | |
| /*display: none;*/ | |
| } | |
| /*clear float left*/ | |
| #clear{ | |
| clear:both; | |
| } | |
| /*fizing jquery autocomplete*/ | |
| .ui-menu-item{ | |
| float:left; | |
| clear: left; | |
| } | |
| /*move down submit button*/ | |
| #gene_search_submit{ | |
| margin-top:5px; | |
| } | |
| #toggle_order{ | |
| margin-top: 10px; | |
| } |
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| d3.json('example_network.json', function(network_data){ | |
| // make global copy of network_data | |
| global_network_data = network_data; | |
| // pass the network data to d3_clustergram | |
| make_d3_clustergram(network_data); | |
| // generate a list of genes for auto complete | |
| //////////////////////////////////////////////// | |
| // get all genes | |
| all_genes = []; | |
| // loop through row_nodes | |
| for (i=0; i<row_nodes.length; i++){ | |
| all_genes.push( row_nodes[i]['name'] ); | |
| }; | |
| // use Jquery autocomplete | |
| //////////////////////////////// | |
| $( "#gene_search_box" ).autocomplete({ | |
| source: all_genes | |
| }); | |
| // submit genes button | |
| $("#gene_search_box").keyup(function (e) { | |
| if (e.keyCode == 13) { | |
| // Do something | |
| // console.log('pressed enter'); | |
| find_gene_in_clust(); | |
| } | |
| }); | |
| }); | |
| // find gene in clustergram | |
| function find_gene_in_clust(){ | |
| // get the searched gene | |
| search_gene = $('#gene_search_box').val(); | |
| if (all_genes.indexOf(search_gene) != -1){ | |
| // zoom and highlight found gene | |
| ///////////////////////////////// | |
| zoom_and_highlight_found_gene(search_gene); | |
| } | |
| }; | |
| // make the svg exp map (one value per tile) | |
| function make_d3_clustergram(network_data) { | |
| // remove old visualization | |
| //////////////////////////////// | |
| d3.select("#main_svg").remove(); | |
| // initialize clustergram variables | |
| initialize_clustergram(network_data) | |
| // display col and row title | |
| d3.select('#row_title').style('display','block'); | |
| d3.select('#col_title').style('display','block'); | |
| // toggle sidebar to make more space for visualization | |
| d3.select('#wrapper').attr('class','toggled'); | |
| // display clustergram_container and clust_instruct_container | |
| d3.select('#clustergram_container').style('display','block'); | |
| d3.select('#clust_instruct_container').style('display','block'); | |
| // shift the footer left | |
| d3.select('#footer_div') | |
| .style('margin-left','0px'); | |
| // // highlight resource types - set up type/color association | |
| // highlight_resource_types(); | |
| // define the variable zoom, a d3 method | |
| zoom = d3.behavior.zoom().scaleExtent([1,real_zoom*zoom_switch]).on('zoom',zoomed); | |
| // initialize matrix | |
| ///////////////////////// | |
| matrix = [] ; | |
| // initialize matrix | |
| row_nodes.forEach( function(tmp,i) { | |
| matrix[i] = d3.range(col_nodes.length).map(function(j) { return {pos_x: j, pos_y: i, value:0, group:0}; }); | |
| }); | |
| // Add information to the matrix | |
| network_data.links.forEach( function(link) { | |
| // transfer link information to the new adj matrix | |
| matrix[link.source][link.target].value = link.value; | |
| // transfer group information to the adj matrix | |
| matrix[link.source][link.target].group = 1; | |
| // transfer color | |
| matrix[link.source][link.target].color = link.color; | |
| }); | |
| // make clustergram visualization | |
| /////////////////////////////////////// | |
| // initailize clust_group with id clust_group | |
| clust_group = d3.select("#svg_div") | |
| .append("svg") | |
| .attr('id', 'main_svg') | |
| // the svg can be larger than the visualization - use svg_height and svg_width | |
| .attr("width", svg_width + margin.left + margin.right + spillover_x_offset) | |
| .attr("height", svg_height + margin.top + margin.bottom) | |
| .attr('border',1) | |
| .call( zoom ) | |
| .append("g") | |
| .attr('id', 'clust_group') | |
| .attr("transform", "translate(" + (margin.left) + "," + (margin.top) + ")"); | |
| // grey background rect for clustergram | |
| d3.select('#clust_group') | |
| .append("rect") | |
| .attr("class", "background") | |
| .attr('id','grey_background') | |
| .attr("width", svg_width) | |
| .attr("height", viz_height); | |
| // make rows | |
| // use matrix for the data join, which contains a two dimensional | |
| // array of objects, each row of this matrix will be passed into the row function | |
| var row_obj = clust_group.selectAll(".row") | |
| .data(matrix) | |
| .enter() | |
| .append("g") | |
| .attr("class", "row") | |
| .attr("transform", function(d, i) { return "translate(0," + y_scale(i) + ")"; }) | |
| .each( row_function ); | |
| // white lines in clustergram | |
| ///////////////////////////////// | |
| // horizontal lines | |
| row_obj.append('line') | |
| .attr('x2', 20*svg_width) | |
| .style('stroke-width', border_width/zoom_switch+'px') | |
| // append vertical line groups | |
| vert_lines = clust_group | |
| .selectAll('.vert_lines') | |
| .data(col_nodes) | |
| .enter() | |
| .append('g') | |
| .attr('class','vert_lines') | |
| .attr('transform', function(d,i){ return 'translate(' + x_scale(i) + ') rotate(-90)'; }) | |
| // add vertical lines | |
| vert_lines | |
| .append('line') | |
| .attr('x1',0) | |
| .attr('x2',-20*viz_height) | |
| .style('stroke-width', border_width+'px') | |
| // row labels | |
| ////////////////////////////////// | |
| // white background rect for row labels | |
| d3.select('#main_svg') | |
| .append('rect') | |
| .attr('fill', 'white') | |
| .attr('width', row_label_width+'px') | |
| .attr('height', '3000px') | |
| .attr('class','white_bars'); | |
| // append group for row labels | |
| d3.select('#main_svg') | |
| .append("g") | |
| .attr('id', 'row_labels') | |
| .attr("transform", "translate(" + row_margin.left + "," + row_margin.top + ")") | |
| // generate and position the row labels | |
| var row_label_obj = d3.select('#row_labels') | |
| .selectAll('.row_label_text') | |
| .data(row_nodes) | |
| .enter() | |
| .append('g') | |
| .attr('class','row_label_text') | |
| .attr('transform', function(d, i) { return "translate(0," + y_scale(i) + ")"; }) | |
| .on('click', reorder_click_row ) | |
| .on('mouseover', function(){ | |
| // highlight text | |
| d3.select(this).select('text') | |
| .style('font-weight','bold'); | |
| }) | |
| .on("mouseout", function mouseout() { | |
| d3.select(this).select('text') | |
| .style('font-weight','normal'); | |
| // reset highlighted col | |
| d3.select('#clicked_row') | |
| .style('font-weight','bold'); | |
| }); | |
| // append row label text | |
| row_label_obj | |
| .append('text') | |
| // !! this will be fixed once I have separate x and y scales | |
| // !! can be improved | |
| .attr('y', y_scale.rangeBand()/2 ) | |
| .attr('dy', y_scale.rangeBand()/4) | |
| .attr('text-anchor','end') | |
| .style('font-size',default_fs_row+'px') | |
| .text(function(d, i) { return d.name; } ) | |
| // append rectangle behind text | |
| row_label_obj | |
| .insert('rect','text') | |
| .attr('x',-10) | |
| .attr('y',0) | |
| .attr('width',10) | |
| .attr('height',10) | |
| .style('opacity',0); | |
| // change the size of the highlighting rects | |
| row_label_obj | |
| .each(function(){ | |
| // get the bounding box of the row label text | |
| var bbox = d3.select(this) | |
| .select('text')[0][0] | |
| .getBBox(); | |
| // use the bounding box to set the size of the rect | |
| d3.select(this) | |
| .select('rect') | |
| .attr('x', bbox.x*0.5) | |
| .attr('y', 0) | |
| .attr('width', bbox.width*0.5) | |
| .attr('height', y_scale.rangeBand()) | |
| .style('fill','yellow') | |
| .style('opacity',0); | |
| }); | |
| // col labels | |
| ////////////////////////////////// | |
| // white background rect for col labels | |
| d3.select('#main_svg') | |
| .append('rect') | |
| .attr('fill', 'white') | |
| .attr('height', col_label_width+'px') | |
| .attr('width', '3000px') | |
| .attr('class','white_bars'); | |
| // append group for column labels | |
| d3.select('#main_svg') | |
| .append("g") | |
| .attr('id', 'col_labels') | |
| .attr("transform", "translate(" + col_margin.left + "," + col_margin.top + ")"); | |
| // offset click group column label | |
| x_offset_click = x_scale.rangeBand()/2 + border_width | |
| // reduce width of rotated rects | |
| reduce_rect_width = x_scale.rangeBand()* 0.36 | |
| // add main column label group | |
| col_label_obj = d3.select('#col_labels') | |
| .selectAll(".col_label_text") | |
| .data(col_nodes) | |
| .enter() | |
| .append("g") | |
| .attr("class", "col_label_text") | |
| .attr("transform", function(d, i) { return "translate(" + x_scale(i) + ") rotate(-90)"; }) | |
| // append group for individual column label | |
| col_label_click = col_label_obj | |
| // append new group for rect and label (not white lines) | |
| .append('g') | |
| .attr('class','col_label_click') | |
| // rotate column labels | |
| .attr('transform', 'translate('+x_scale.rangeBand()/2+','+ x_offset_click +') rotate(45)') | |
| .on('click', reorder_click_col ) | |
| .on('mouseover', function(){ | |
| // highlight text | |
| d3.select(this).select('text') | |
| .style('font-weight','bold'); | |
| }) | |
| .on("mouseout", function mouseout() { | |
| // d3.selectAll("text").classed("active", false); | |
| d3.select(this).select('text') | |
| .style('font-weight','normal'); | |
| // reset highlighted col | |
| d3.select('#clicked_col') | |
| .style('font-weight','bold'); | |
| }); | |
| // add column label | |
| col_label_click | |
| .append("text") | |
| .attr("x", 0) | |
| .attr("y", x_scale.rangeBand() / 2) | |
| .attr('dx',2*border_width) | |
| // .attr("dy", ".32em") | |
| .attr("text-anchor", "start") | |
| .attr('full_name',function(d) { return d.name } ) | |
| .style('font-size',default_fs_col+'px') | |
| // remove underscores from name | |
| .text(function(d, i) { return d.name.replace(/_/g, ' ') ; }); | |
| // append rectangle behind text | |
| col_label_click | |
| .insert('rect','text') | |
| .attr('x',10) | |
| .attr('y',0) | |
| .attr('width',10) | |
| .attr('height',10) | |
| .style('opacity',0); | |
| // change the size of the highlighting rects | |
| col_label_click | |
| .each(function(){ | |
| // get the bounding box of the row label text | |
| var bbox = d3.select(this) | |
| .select('text')[0][0] | |
| .getBBox(); | |
| // use the bounding box to set the size of the rect | |
| d3.select(this) | |
| .select('rect') | |
| .attr('x', bbox.x*1.25) | |
| .attr('y', 0) | |
| .attr('width', bbox.width*1.25) | |
| // used teh reduced rect width for the columsn | |
| // reduced because thee rects are slanted | |
| .attr('height', x_scale.rangeBand()*0.6) | |
| // .attr('height', reduce_rect_width) | |
| .style('fill','yellow') | |
| .style('opacity',0); | |
| }); | |
| // add triangle under rotated labels | |
| col_label_click | |
| .append('path') | |
| .style('stroke-width',0) | |
| .attr('d', function(d) { | |
| // x and y are flipped since its rotated | |
| origin_y = - border_width | |
| start_x = 0; | |
| final_x = x_scale.rangeBand() - reduce_rect_width ; | |
| start_y = -(x_scale.rangeBand() - reduce_rect_width + border_width) ; | |
| final_y = -border_width; | |
| output_string = 'M '+origin_y+',0 L ' + start_y + ',' + start_x + ', L ' + final_y + ','+final_x+' Z'; | |
| return output_string; | |
| }) | |
| .attr('fill','#eee') | |
| // change the colors of the triangles | |
| // .attr('fill', function(d) { | |
| // // look up color using data_group | |
| // inst_color = res_color_dict[d.name]; | |
| // return inst_color; | |
| // }); | |
| // Rects to hide spillover | |
| /////////////////////////////// | |
| // white rect to cover excess labels | |
| d3.select('#main_svg') | |
| .append('rect') | |
| .attr('fill', 'white') | |
| .attr('width', row_label_width+'px') | |
| .attr('height', col_label_width+'px') | |
| .attr('id','top_left_white'); | |
| // hide spillover from right | |
| d3.select('#main_svg') | |
| .append('rect') | |
| .attr('fill', 'white') | |
| .attr('width', '200px') | |
| .attr('height', '3000px') | |
| .attr('transform', function() { | |
| tmp_left = margin.left + svg_width; | |
| // compensate for margin | |
| tmp_top = margin.top - 5; | |
| return 'translate('+tmp_left+','+tmp_top+')' | |
| }) | |
| .attr('class','white_bars'); | |
| // hide spillover from slanged column labels | |
| d3.select('#main_svg') | |
| .append('path') | |
| .style('stroke-width','0') | |
| // mini-language for drawing path in d3, used to draw triangle | |
| .attr('d', 'M 0,0 L 500,-500, L 500,0 Z') | |
| .attr('fill','white') | |
| .attr('id','slant_traingle') | |
| .attr('transform', function(){ | |
| tmp_left = (margin.left + svg_width ); | |
| tmp_top = col_label_width ; | |
| return 'translate('+tmp_left+','+tmp_top+')' | |
| }) | |
| // initialize zoom and translate | |
| /////////////////////////////////// | |
| // initialize translate vector to compensate for label margins | |
| zoom.translate([ margin.left, margin.top]); | |
| // resize window | |
| d3.select(window).on('resize', timeout_resize); | |
| // disable double-click zoom: double click should reset zoom level | |
| // do this for all svg elements | |
| d3.selectAll("svg").on("dblclick.zoom", null); | |
| // double click to reset zoom - add transition | |
| d3.select('#main_svg') | |
| // for some reason, do not put brackets in these functions | |
| .on('dblclick', function(){ | |
| // apply the following two translate zoom to reset zoom | |
| // programatically | |
| two_translate_zoom(0,0,1) | |
| } ); | |
| }; | |
| // row function | |
| function row_function(row_data) { | |
| // generate tiles in the current row | |
| cell = d3.select(this) | |
| // data join | |
| .selectAll(".cell") | |
| .data( row_data ) | |
| .enter() | |
| .append("rect") | |
| .attr('class', 'cell') | |
| .attr("x", function(d) { return x_scale(d.pos_x); }) | |
| .attr("width", x_scale.rangeBand()) | |
| .attr("height", y_scale.rangeBand()) | |
| .style("fill-opacity", function(d) { | |
| // calculate output opacity using the opacity scale | |
| output_opacity = opacity_scale( Math.abs(d.value) ); | |
| return output_opacity ; | |
| }) | |
| // switch the color based on up/dn enrichment | |
| .style('fill', function(d) { | |
| // console.log(d) | |
| return d.value > 0 ? '#FF0000' : '#1C86EE' ; | |
| // if (d.value != 0){ | |
| // inst_color = d.color; | |
| // } | |
| // else{ | |
| // inst_color = null; | |
| // } | |
| // return inst_color ; | |
| } ) | |
| .on("mouseover", function(p) { | |
| d3.selectAll(".row_label_text text").classed("active", function(d, i) { return i == p.pos_y; }); | |
| d3.selectAll(".col_label_text text").classed("active", function(d, i) { return i == p.pos_x; }); | |
| }) | |
| .on("mouseout", function mouseout() { | |
| d3.selectAll("text").classed("active", false); | |
| }) | |
| }; | |
| function reorder_clust_rank(order_type) { | |
| // load orders | |
| if ( order_type == 'clust' ){ | |
| // order by enrichment | |
| x_scale.domain(orders.clust_row); | |
| y_scale.domain(orders.clust_col); | |
| } | |
| else if (order_type == 'rank'){ | |
| // order by enrichment | |
| x_scale.domain(orders.rank_row); | |
| y_scale.domain(orders.rank_col); | |
| }; | |
| // define the t variable as the transition function | |
| var t = clust_group.transition().duration(2500); | |
| // reorder matrix | |
| t.selectAll(".row") | |
| .attr("transform", function(d, i) { return "translate(0," + y_scale(i) + ")"; }) | |
| .selectAll(".cell") | |
| .attr('x', function(d){ | |
| return x_scale(d.pos_x); | |
| }) | |
| // Move Row Labels | |
| d3.select('#row_labels').selectAll('.row_label_text') | |
| .transition().duration(2500) | |
| .attr('transform', function(d, i) { return 'translate(0,' + y_scale(i) + ')'; }); | |
| // t.selectAll(".column") | |
| d3.select('#col_labels').selectAll(".col_label_text") | |
| .transition().duration(2500) | |
| .attr("transform", function(d, i) { | |
| return "translate(" + x_scale(i) + ")rotate(-90)"; | |
| }); | |
| }; | |
| // initialize clustergram: size, scales, etc. | |
| function initialize_clustergram(network_data){ | |
| // move network_data information into global variables | |
| col_nodes = network_data.col_nodes ; | |
| row_nodes = network_data.row_nodes ; | |
| inst_links = network_data.links; | |
| // define screen limits | |
| min_screen_width = 800; | |
| max_screen_width = 2500; | |
| // define screen limits | |
| min_viz_width = 400; | |
| max_viz_width = 2000; | |
| min_viz_height = 600; | |
| max_viz_height = 1500; | |
| // initialize visualization size | |
| set_visualization_size(); | |
| // font size controls | |
| // scale default font size: input domain is the number of nodes | |
| min_node_num = 10; | |
| max_node_num = 2000; | |
| // // scale col and row font size | |
| // /////////////////////////////// | |
| // // max and min font sizes | |
| // min_fs = 0.01 * scale_fs_screen(screen_width); | |
| // max_fs = 15 * scale_fs_screen(screen_width); | |
| // scale only col font size | |
| /////////////////////////////// | |
| // max and min font sizes | |
| min_fs = 0.05; | |
| max_fs = 15; | |
| // output range is the font size | |
| scale_font_size = d3.scale.log().domain([min_node_num,max_node_num]).range([max_fs,min_fs]).clamp('true'); | |
| // controls how much the font size is increased by zooming when the number of nodes is at its max | |
| // and zooming is required | |
| // 1: do not increase font size while zooming | |
| // 0: increase font size while zooming | |
| // allow some increase in font size when zooming | |
| min_fs_zoom = 0.95; | |
| // allow full increase in font size when zooming | |
| max_fs_zoom = 0.0; | |
| // define the scaling for the reduce font size factor | |
| scale_reduce_font_size_factor = d3.scale.log().domain([min_node_num,max_node_num]).range([min_fs_zoom,max_fs_zoom]).clamp('true'); | |
| // // define the scaling for the zoomability of the adjacency matrix | |
| // scale_zoom = d3.scale.log().domain([min_node_num,max_node_num]).range([2,17]).clamp('true'); | |
| // define screen width font size scale | |
| // having a small screen width should reduce the font size of the columns | |
| // this will be compensated by increasing the available real zoom | |
| scale_fs_screen_width = d3.scale.linear().domain( [min_viz_width,max_viz_width]).range([0.75,1.15]).clamp('true'); | |
| scale_fs_screen_height = d3.scale.linear().domain([min_viz_width,max_viz_width]).range([0.75,1.15]).clamp('true'); | |
| // the default font sizes are set here | |
| default_fs_row = scale_font_size(row_nodes.length)* scale_fs_screen_height(viz_height); | |
| // the colum font size is scaled by the width | |
| default_fs_col = scale_font_size(col_nodes.length)* scale_fs_screen_width(viz_width); | |
| // correct for forcing the tiles to be squares - if they are forced, then use the col font size scaling on the rows | |
| if (force_square == 1){ | |
| // scale the row font size by the col scaling | |
| default_fs_row = default_fs_col; | |
| }; | |
| // calculate the reduce font-size factor: 0 for no reduction in font size and 1 for full reduction of font size | |
| reduce_font_size_factor_row = scale_reduce_font_size_factor(row_nodes.length); | |
| reduce_font_size_factor_col = scale_reduce_font_size_factor(col_nodes.length); | |
| // set up the real zoom (2d zoom) as a function of the number of col_nodes | |
| // since these are the nodes that are zoomed into in 2d zooming | |
| real_zoom_scale_col = d3.scale.linear().domain([min_node_num,max_node_num]).range([2,5]).clamp('true'); | |
| // scale the zoom based on the screen size | |
| // smaller screens can zoom in more, compensates for reduced font size with small screen | |
| real_zoom_scale_screen = d3.scale.linear().domain([min_screen_width,max_screen_width]).range([2,1]).clamp('true'); | |
| // calculate the zoom factor - the more nodes the more zooming allowed | |
| real_zoom = real_zoom_scale_col(col_nodes.length)*real_zoom_scale_screen(screen_width); | |
| // set opacity scale | |
| max_link = _.max( inst_links, function(d){ return Math.abs(d.value) } ) | |
| opacity_scale = d3.scale.linear().domain([0, Math.abs(max_link.value) ]).clamp(true).range([0.0,1.0]) ; | |
| }; | |
| function set_visualization_size(){ | |
| // find the label with the most characters and use it to adjust the row and col margins | |
| row_max_char = _.max(row_nodes, function(inst) {return inst.name.length;}).name.length; | |
| col_max_char = _.max(col_nodes, function(inst) {return inst.name.length;}).name.length; | |
| // define label scale parameters: the more characters in the longest name, the larger the margin | |
| min_num_char = 5; | |
| max_num_char = 40; | |
| min_label_width = 60; | |
| max_label_width = 200; | |
| label_scale = d3.scale.linear().domain([min_num_char,max_num_char]).range([min_label_width,max_label_width]).clamp('true'); | |
| // set col_label_width and row_label_width | |
| row_label_width = label_scale(row_max_char) ; | |
| triangle_space = 30; | |
| col_label_width = label_scale(col_max_char) + triangle_space ; | |
| // distance between labels and clustergram | |
| label_margin = 5; | |
| // Margins | |
| col_margin = { top:col_label_width - label_margin, right:0, bottom:0, left:row_label_width }; | |
| row_margin = { top:col_label_width, right:0, bottom:0, left:row_label_width-label_margin }; | |
| margin = { top:col_label_width, right:0, bottom:0, left:row_label_width }; | |
| // from http://stackoverflow.com/questions/16265123/resize-svg-when-window-is-resized-in-d3-js | |
| x_window = window.innerWidth ; | |
| y_window = window.innerHeight ; | |
| // set wrapper width and height | |
| d3.select('#wrapper').style('width', x_window); | |
| d3.select('#wrapper').style('height',y_window); | |
| // initalize clutergram container | |
| // | |
| // get screen width | |
| screen_width = Number(d3.select('#wrapper').style('width').replace('px','')); | |
| // get screen height | |
| screen_height = Number(d3.select('#wrapper').style('height').replace('px','')); | |
| // define offsets for permanent row and col margins | |
| // takes into consideration sidebar | |
| // reducing sidebar width, row_offset used to be 280 when left margin was 260 | |
| // now, rowoffset is 240 when left margin is reduced to 220 (-40px) | |
| // further reducing width of from 220 to 210px - left margin will be 230px | |
| container_row_offset = 230; | |
| // takes into consideration footer and header margin | |
| container_col_offset = 50; | |
| // adjust container with border | |
| // define width and height of clustergram container | |
| width_clust_container = screen_width - container_row_offset; | |
| height_clust_container = screen_height - container_col_offset; | |
| // Clustergram Container | |
| /////////////////////////////// | |
| // set clustergram_container and clust_and_row_container dimensions | |
| // clustergram_container | |
| d3.select('#clustergram_container').style('width', width_clust_container+'px') | |
| d3.select('#clustergram_container').style('height', height_clust_container+'px') | |
| // clust_and_row_container | |
| d3.select('#clust_and_row_container').style('width',width_clust_container+'px') | |
| d3.select('#clust_and_row_container').style('height',height_clust_container+'px') | |
| // SVG | |
| //////////////// | |
| // define offset for svg | |
| // compenstates for permanent row and column labels as well | |
| // as x spillover | |
| spillover_x_offset = label_scale(col_max_char)* 0.8 ; | |
| svg_x_offset = 50 + spillover_x_offset; | |
| svg_y_offset = 50; | |
| // svg size: less than container size | |
| // subtract fixed length for permanent col and row labels and variable length for specific col and row labels | |
| svg_width = width_clust_container - svg_x_offset - row_label_width ; | |
| svg_height = height_clust_container - svg_y_offset - col_label_width ; | |
| // define a visualization size, which may be smaller than the svg size if | |
| // there are a small number of rows | |
| // or if there are more columns than rows | |
| ////////////////////////////////////////////////// | |
| // viz_width | |
| //////////////////////// | |
| // set up a scale that will prevent the visualization | |
| // from stretching a few rows across the entire width | |
| prevent_col_stetch = d3.scale.linear().domain([1,20]).range([0.05,1]).clamp('true'); | |
| viz_width = svg_width * prevent_col_stetch(col_nodes.length) ; | |
| // viz_height | |
| //////////////// | |
| // ensure that width of rects is not less than height | |
| if (col_nodes.length > row_nodes.length){ | |
| // scale the height | |
| viz_height = svg_width*(row_nodes.length/col_nodes.length); | |
| // keep track of whether or not a force square has occurred | |
| // so that I can adjust the font accordingly | |
| // here it has | |
| force_square = 1; | |
| // make sure that this scaling does not cause the viz to be taller | |
| // than the svg | |
| if (viz_height > svg_height){ | |
| // make the height equal to the width, to force square tiles - rather than thin tiles that | |
| // are taller than they are wide | |
| viz_height = svg_height; | |
| // keep track of whether or not a force square has occurred | |
| // here it has not | |
| force_square = 0; | |
| }; | |
| } | |
| // use the unaltered height | |
| else{ | |
| // the height will be calculated normally - leading to wide tiles | |
| viz_height = svg_height; | |
| // keep track of whether or not a force square has occurred | |
| // here it has not | |
| force_square = 0; | |
| }; | |
| // scaling functions used to position tiles | |
| x_scale = d3.scale.ordinal().rangeBands([0, viz_width]) ; | |
| y_scale = d3.scale.ordinal().rangeBands([0, viz_height]); | |
| // Sort rows and columns | |
| orders = { | |
| name: d3.range(col_nodes.length).sort(function(a, b) { return d3.ascending( col_nodes[a].name, col_nodes[b].name); }), | |
| // rank | |
| rank_row: d3.range(col_nodes.length).sort(function(a, b) { return col_nodes[b].rank - col_nodes[a].rank; }), | |
| rank_col: d3.range(row_nodes.length).sort(function(a, b) { return row_nodes[b].rank - row_nodes[a].rank; }), | |
| // clustered | |
| // the clust order is stored under sort !! | |
| clust_row: d3.range(col_nodes.length).sort(function(a, b) { return col_nodes[b].sort - col_nodes[a].sort; }), | |
| clust_col: d3.range(row_nodes.length).sort(function(a, b) { return row_nodes[b].sort - row_nodes[a].sort; }) | |
| }; | |
| // Assign the default sort order for the columns | |
| x_scale.domain(orders.clust_row); | |
| y_scale.domain(orders.clust_col); | |
| // define border width | |
| border_width = x_scale.rangeBand()/16.66; | |
| // define the zoom switch value - use viz_width and viz_height | |
| // switch from 1 to 2d zoom | |
| zoom_switch = (viz_width/col_nodes.length)/(viz_height/row_nodes.length); | |
| }; | |
| // recalculate the size of the visualization | |
| // and remake the clustergram | |
| function reset_visualization_size(){ | |
| // recalculate the size | |
| set_visualization_size(); | |
| // reset zoom and translate | |
| zoom.scale(1).translate([margin.left, margin.top]); | |
| // pass the network data to d3_clustergram | |
| make_d3_clustergram(global_network_data); | |
| // // turn off the wait sign | |
| // $.unblockUI(); | |
| }; | |
| // define zoomed function | |
| function zoomed() { | |
| // gather transformation components | |
| ///////////////////////////////////// | |
| // gather zoom components | |
| zoom_x = d3.event.scale; | |
| zoom_y = d3.event.scale; | |
| // gather translate vector components | |
| trans_x = d3.event.translate[0] - margin.left; | |
| trans_y = d3.event.translate[1] - margin.top; | |
| // apply transformation: no transition duration when zooming with mouse | |
| apply_transformation(trans_x, trans_y, zoom_x, zoom_y, 0); | |
| // reset highlighted col | |
| d3.select('#clicked_col') | |
| // .style('font-size',default_fs_col*1.25) | |
| .style('font-weight','bold'); | |
| }; | |
| // apply transformation | |
| function apply_transformation(trans_x, trans_y, zoom_x, zoom_y, duration){ | |
| // define d3 scale | |
| d3_scale = zoom_x ; | |
| // y - rules | |
| /////////////////////////////////////////////////// | |
| // available panning room in the y direction | |
| // multiple extra room (zoom - 1) by the width | |
| // always defined in the same way | |
| pan_room_y = (d3_scale - 1) * svg_height ; | |
| // if the transformation is from a gene search, the remove pan_room_y restriction | |
| if (duration > 0){ | |
| // set pan_room_y to svg_height - removing restriction | |
| pan_room_y = svg_height; | |
| }; | |
| // do not translate if translate in y direction is positive | |
| if (trans_y >= 0 ) { | |
| console.log('\nrestrict panning in the positive y direction') | |
| console.log(trans_y) | |
| // restrict transformation parameters | |
| // no panning in either direction | |
| trans_y = 0; | |
| } | |
| // restrict y pan to pan_room_y if necessary | |
| else if (trans_y <= -pan_room_y) { | |
| trans_y = -pan_room_y; | |
| console.log('\nrestrict y panning based on y panning ') | |
| }; | |
| // x - rules | |
| /////////////////////////////////////////////////// | |
| // zoom in y direction only - translate in y only | |
| if (d3_scale < zoom_switch) { | |
| // no x translate or zoom | |
| trans_x = 0; | |
| zoom_x = 1; | |
| } | |
| // zoom in both directions | |
| // scale is greater than zoom_switch | |
| else{ | |
| // available panning room in the x direction | |
| // multiple extra room (zoom - 1) by the width | |
| pan_room_x = (d3_scale/zoom_switch - 1) * svg_width ; | |
| // no panning in the positive direction | |
| if (trans_x > 0){ | |
| // restrict transformation parameters | |
| // no panning in the x direction | |
| trans_x = 0; | |
| // set zoom_x | |
| zoom_x = d3_scale/zoom_switch; | |
| } | |
| // restrict panning to pan_room_x | |
| else if (trans_x <= -pan_room_x){ | |
| // restrict transformation parameters | |
| // no panning in the x direction | |
| trans_x = -pan_room_x; | |
| // set zoom_x | |
| zoom_x = d3_scale/zoom_switch; | |
| } | |
| // allow two dimensional panning | |
| else{ | |
| // restrict transformation parameters | |
| // set zoom_x | |
| zoom_x = d3_scale/zoom_switch; | |
| }; | |
| }; | |
| // apply transformation and reset translate vector | |
| // the zoom vector (zoom.scale) never gets reset | |
| /////////////////////////////////////////////////// | |
| // translate clustergram | |
| clust_group | |
| .attr('transform','translate(' + [ margin.left + trans_x, margin.top + trans_y ] + ') scale('+ zoom_x +',' + zoom_y + ')'); | |
| // transform row labels | |
| d3.select('#row_labels') | |
| .attr('transform','translate(' + [row_margin.left , margin.top + trans_y] + ') scale(' + zoom_y + ')'); | |
| // transform col labels | |
| // move down col labels as zooming occurs, subtract trans_x - 20 almost works | |
| d3.select('#col_labels') | |
| .attr('transform','translate(' + [col_margin.left + trans_x , col_margin.top] + ') scale(' + zoom_x + ')'); | |
| // reset translate vector - add back margins to trans_x and trans_y | |
| zoom | |
| .translate([ trans_x + margin.left, trans_y + margin.top]); | |
| // Font Sizes | |
| ////////////////// | |
| // reduce the font size by dividing by some part of the zoom | |
| // if reduce_font_size_factor_ is 1, then the font will be divided by the whole zoom - and the labels will not increase in size | |
| // if reduce_font_size_factor_ is 0, then the font will be divided 1 - and the labels will increase cuction of the font size | |
| reduce_font_size = d3.scale.linear().domain([0,1]).range([1,zoom_y]).clamp('true'); | |
| // scale down the font to compensate for zooming | |
| fin_font = default_fs_row/(reduce_font_size(reduce_font_size_factor_row)); | |
| // add back the 'px' to the font size | |
| fin_font = fin_font + 'px'; | |
| // change the font size of the labels | |
| d3.selectAll('.row_label_text') | |
| .select('text') | |
| .style('font-size', fin_font); | |
| // re-size of the highlighting rects | |
| d3.select('#row_labels') | |
| .each(function(){ | |
| // get the bounding box of the row label text | |
| var bbox = d3.select(this) | |
| .select('text')[0][0] | |
| .getBBox(); | |
| // use the bounding box to set the size of the rect | |
| d3.select(this) | |
| .select('rect') | |
| .attr('x', bbox.x*0.5) | |
| .attr('y', 0) | |
| .attr('width', bbox.width*0.5) | |
| .attr('height', y_scale.rangeBand()) | |
| .style('fill','yellow'); | |
| }); | |
| // reduce font-size to compensate for zoom | |
| // calculate the recuction of the font size | |
| reduce_font_size = d3.scale.linear().domain([0,1]).range([1,zoom_x]).clamp('true'); | |
| // scale down the font to compensate for zooming | |
| fin_font = default_fs_col/(reduce_font_size(reduce_font_size_factor_col)); | |
| // add back the 'px' to the font size | |
| fin_font = fin_font + 'px'; | |
| // change the font size of the labels | |
| d3.selectAll('.col_label_text') | |
| .select('text') | |
| .style('font-size', fin_font); | |
| // change the size of the highlighting rects | |
| // col_label_click | |
| d3.select('#col_labels') | |
| .each(function(){ | |
| // get the bounding box of the row label text | |
| var bbox = d3.select(this) | |
| .select('text')[0][0] | |
| .getBBox(); | |
| // use the bounding box to set the size of the rect | |
| d3.select(this) | |
| .select('rect') | |
| .attr('x', bbox.x*1.25) | |
| .attr('y', 0) | |
| .attr('width', bbox.width * 1.25) | |
| // used teh reduced rect width for the columsn | |
| // reduced because thee rects are slanted | |
| .attr('height', x_scale.rangeBand()*0.6) | |
| .style('fill','yellow') | |
| .style('opacity',0); | |
| }); | |
| }; | |
| // reorder columns with row click | |
| function reorder_click_row(d,i){ | |
| // get inst row (gene) | |
| inst_gene = d3.select(this).select('text').text(); | |
| // highlight clicked column | |
| // first un-highlight all others | |
| d3.selectAll('.rol_label_text').select('text') | |
| .style('font-weight','normal'); | |
| // remove previous id | |
| d3.select('#clicked_row') | |
| .attr('id',''); | |
| // highlight current | |
| d3.select(this).select('text') | |
| .style('font-weight','bold') | |
| .attr('id','clicked_row'); | |
| // find the row number of this term from row_nodes | |
| // gather row node names | |
| tmp_arr = [] | |
| for (i=0; i<row_nodes.length; i++){ | |
| tmp_arr.push(row_nodes[i].name); | |
| } | |
| // find index | |
| inst_row = _.indexOf( tmp_arr, inst_gene ); | |
| // gather the values of the input genes | |
| tmp_arr = []; | |
| for (j=0; j<col_nodes.length; j++) { | |
| tmp_arr.push(matrix[inst_row][j].value); | |
| } | |
| // sort the rows | |
| tmp_sort = d3.range( tmp_arr.length ).sort(function(a, b) { return tmp_arr[b] - tmp_arr[a]; }) | |
| // resort the columns (resort x) | |
| x_scale.domain(tmp_sort); | |
| // reorder | |
| //////////////////// | |
| // define the t variable as the transition function | |
| var t = clust_group.transition().duration(2500); | |
| // reorder matrix | |
| t.selectAll(".cell") | |
| .attr('x', function(d){ | |
| return x_scale(d.pos_x); | |
| }); | |
| // Move Row Labels | |
| d3.select('#col_labels').selectAll(".col_label_text") | |
| .transition().duration(2500) | |
| .attr("transform", function(d, i) { | |
| return "translate(" + x_scale(i) + ")rotate(-90)"; | |
| }); | |
| // // zoom into and highlight selected row | |
| // zoom_and_highlight_found_gene(inst_gene); | |
| }; | |
| // reorder rows with column click | |
| function reorder_click_col(d,i){ | |
| // get inst col (term) | |
| inst_term = d3.select(this).select('text').attr('full_name') | |
| // highlight clicked column | |
| // first un-highlight all others | |
| d3.selectAll('.col_label_text').select('text') | |
| .style('font-weight','normal'); | |
| // remove previous id | |
| d3.select('#clicked_col') | |
| .attr('id',''); | |
| // highlight current | |
| d3.select(this).select('text') | |
| .style('font-weight','bold') | |
| .attr('id','clicked_col'); | |
| // find the column number of this term from col_nodes | |
| // gather column node names | |
| tmp_arr = [] | |
| for (i=0; i<col_nodes.length; i++){ | |
| tmp_arr.push(col_nodes[i].name); | |
| }; | |
| // find index | |
| inst_col = _.indexOf( tmp_arr, inst_term ); | |
| // gather the values of the input genes | |
| tmp_arr = []; | |
| for (i=0; i<row_nodes.length; i++) { | |
| tmp_arr.push(matrix[i][inst_col].value); | |
| }; | |
| // sort the rows | |
| tmp_sort = d3.range( tmp_arr.length).sort(function(a, b) { return tmp_arr[b] - tmp_arr[a]; }) | |
| // resort rows - y axis | |
| y_scale.domain(tmp_sort); | |
| // reorder | |
| // define the t variable as the transition function | |
| var t = clust_group.transition().duration(2500); | |
| // reorder matrix | |
| t.selectAll(".row") | |
| .attr("transform", function(d, i) { return "translate(0," + y_scale(i) + ")"; }) | |
| .selectAll(".cell") | |
| .attr('x', function(d){ | |
| return x_scale(d.pos_x); | |
| }) | |
| // Move Row Labels | |
| // | |
| d3.select('#row_labels').selectAll('.row_label_text') | |
| .transition().duration(2500) | |
| .attr('transform', function(d, i) { return 'translate(0,' + y_scale(i) + ')'; }); | |
| // t.selectAll(".column") | |
| d3.select('#col_labels').selectAll(".col_label_text") | |
| .transition().duration(2500) | |
| .attr("transform", function(d, i) { | |
| return "translate(" + x_scale(i) + ")rotate(-90)"; | |
| }); | |
| // highlight selected column | |
| /////////////////////////////// | |
| // unhilight and unbold all columns (already unbolded earlier) | |
| d3.selectAll('.col_label_text') | |
| .select('rect') | |
| .style('opacity',0); | |
| // highlight column name | |
| d3.select(this) | |
| .select('rect') | |
| .style('opacity',1); | |
| }; | |
| // resize clustergram with screensize change | |
| var doit; | |
| function timeout_resize(){ | |
| // clear timeout | |
| clearTimeout(doit); | |
| // // set up wait message before request is made | |
| // $.blockUI({ css: { | |
| // border: 'none', | |
| // padding: '15px', | |
| // backgroundColor: '#000', | |
| // '-webkit-border-radius': '10px', | |
| // '-moz-border-radius': '10px', | |
| // opacity: .8, | |
| // color: '#fff' | |
| // } }); | |
| doit = setTimeout( reset_visualization_size, 500) ; | |
| }; | |
| // interpolate pan and zoom | |
| function interpolate_pan_zoom(pan_dx, pan_dy, fin_zoom){ | |
| }; | |
| function two_translate_zoom(pan_dx, pan_dy, fin_zoom){ | |
| console.log('two_translate_zoom') | |
| console.log('pan_dx: '+String(pan_dx)) | |
| console.log('pan_dy: '+String(pan_dy)) | |
| console.log('fin_zoom: '+String(fin_zoom)) | |
| // define the commonly used variable half_height | |
| var half_height = viz_height/2 ; | |
| // y pan room, the pan room has to be less than half_height since | |
| // zooming in on a gene that is near the top of the clustergram also causes | |
| // panning out of the visible region | |
| var y_pan_room = ((half_height)/zoom_switch); | |
| // prevent visualization from panning down too much | |
| // when zooming into genes near the top of the clustergram | |
| if (pan_dy >= half_height - y_pan_room){ | |
| console.log('restricting pan down') | |
| // prevent the clustergram from panning down too much | |
| // if the amount of panning is equal to the half_height then it needs to be reduced | |
| // effectively, the the visualization needs to be moved up (negative) by some factor | |
| // of the half width of the visualization. If there was no zooming involved, then the | |
| // visualization would be centered first, then panned to center the top term, then | |
| // the correction would re-center it. However, because of the zooming the offset is | |
| // reduced by the zoom factor (this is because the panning is occurring on something | |
| // that will be zoomed into - this is why the pan_dy value is not scaled in the two | |
| // translate transformations, but it has to be scaled afterwards to set the translate | |
| // vector) | |
| // pan_dy = half_height - (half_height)/zoom_switch | |
| // if pan_dy is greater than the pan room, then panning has to be restricted | |
| // start by shifting back up (negative) by half_height/zoom_switch then shift bak down | |
| // by the difference between half_height and pan_dy (so that the top of the clustergram is | |
| // visible) | |
| var shift_top_viz = half_height - pan_dy ; | |
| var shift_up_viz = - half_height/zoom_switch + shift_top_viz ; | |
| // reduce pan_dy so that the visualization does not get panned to far down | |
| pan_dy = pan_dy + shift_up_viz ; | |
| }; | |
| // prevent visualization from panning up too much | |
| // when zooming into genes at the bottom of the clustergram | |
| if (pan_dy < -(half_height - y_pan_room) ){ | |
| console.log('restricting pan up') | |
| var shift_top_viz = half_height + pan_dy ; | |
| // does not seem to be needed | |
| ///////// | |
| // move up by one row height | |
| // var move_up_one_row = y_scale.rangeBand(); | |
| // // do not move up one row if the clustergram is square | |
| // if (zoom_switch == 1){ | |
| // move_up_one_row = 0; | |
| // }; | |
| var shift_up_viz = half_height/zoom_switch - shift_top_viz; //- move_up_one_row; | |
| // reduce pan_dy so that the visualization does not get panned to far down | |
| pan_dy = pan_dy + shift_up_viz ; | |
| }; | |
| // will improve this !! | |
| zoom_y = fin_zoom; | |
| zoom_x = 1; | |
| // search duration - the duration of zooming and panning | |
| search_duration =700; | |
| // center_y | |
| center_y = -(zoom_y -1)*half_height; | |
| // console.log('\ncenter_y\t'+center_y+'\n') | |
| // console.log('\npan_dy\t'+pan_dy+'\n') | |
| // transform clsut group | |
| clust_group | |
| .transition() | |
| .duration(search_duration) | |
| // first apply the margin transformation | |
| // then zoom, then apply the final transformation | |
| .attr('transform', 'translate(' + [ margin.left, margin.top + center_y ] + ')'+' scale('+ 1 +',' + zoom_y + ')'+'translate(' + [ pan_dx, pan_dy ] + ')'); | |
| // transform row labels | |
| d3.select('#row_labels') | |
| .transition() | |
| .duration(search_duration) | |
| .attr('transform', 'translate(' + [ row_margin.left, margin.top + center_y ] + ')'+' scale('+ zoom_y +',' + zoom_y + ')'+'translate(' + [ 0, pan_dy ] + ')'); | |
| // transform col labels | |
| // move down col labels as zooming occurs, subtract trans_x - 20 almost works | |
| d3.select('#col_labels') | |
| .transition() | |
| .duration(search_duration) | |
| // .attr('transform','translate(' + [col_margin.left + pan_dx , col_margin.top] + ') scale(' + 1 + ')'); | |
| .attr('transform', 'translate(' + [ col_margin.left, col_margin.top ] + ')'+' scale('+ 1 +',' + 1 + ')'+'translate(' + [ pan_dx, 0 ] + ')'); | |
| // Font Sizes | |
| ////////////////// | |
| // reduce font-size to compensate for zoom | |
| // calculate the recuction of the font size | |
| reduce_font_size = d3.scale.linear().domain([0,1]).range([1,zoom_y]).clamp('true'); | |
| // scale down the font to compensate for zooming | |
| fin_font = default_fs_row/(reduce_font_size(reduce_font_size_factor_row)); | |
| // add back the 'px' to the font size | |
| fin_font = fin_font + 'px'; | |
| // change the font size of the labels | |
| d3.selectAll('.row_label_text') | |
| .transition() | |
| .duration(search_duration) | |
| .select('text') | |
| .style('font-size', fin_font); | |
| // resize the highlighting bar when performing two transition zoom | |
| // re-size of the highlighting rects | |
| d3.select('#row_labels') | |
| .each(function(){ | |
| // get the bounding box of the row label text | |
| var bbox = d3.select(this) | |
| .select('text')[0][0] | |
| .getBBox(); | |
| // use the bounding box to set the size of the rect | |
| d3.select(this) | |
| .select('rect') | |
| .attr('x', bbox.x*0.5) | |
| .attr('y', 0) | |
| .attr('width', bbox.width*0.5) | |
| .attr('height', y_scale.rangeBand()) | |
| .style('fill','yellow'); | |
| }); | |
| // reduce font-size to compensate for zoom | |
| // calculate the recuction of the font size | |
| reduce_font_size = d3.scale.linear().domain([0,1]).range([1,zoom_x]).clamp('true'); | |
| // scale down the font to compensate for zooming | |
| fin_font = default_fs_col/(reduce_font_size(reduce_font_size_factor_col)); | |
| // add back the 'px' to the font size | |
| fin_font = fin_font + 'px'; | |
| // change the font size of the labels | |
| d3.selectAll('.col_label_text') | |
| .transition() | |
| .duration(search_duration) | |
| .select('text') | |
| .style('font-size', fin_font); | |
| // set y translate: center_y is positive, positive moves the visualization down | |
| // the translate vector has the initial margin, the first y centering, and pan_dy | |
| // times the scaling zoom_y | |
| var net_y_offset = margin.top + center_y + pan_dy * zoom_y ; | |
| // reset the zoom translate and zoom | |
| zoom.scale(zoom_y); | |
| zoom.translate([ pan_dx, net_y_offset]) | |
| }; | |
| // zoom into and highlight the found the gene | |
| function zoom_and_highlight_found_gene(search_gene){ | |
| // unhighlight and unbold all genes | |
| d3.selectAll('.row_label_text') | |
| .select('text') | |
| .style('font-weight','normal'); | |
| d3.selectAll('.row_label_text') | |
| .select('rect') | |
| .style('opacity',0); | |
| // find the index of the gene | |
| inst_gene_index = _.indexOf( all_genes, search_gene ); | |
| // get y position | |
| inst_y_pos = y_scale(inst_gene_index) ; | |
| // make row name bold | |
| d3.selectAll('.row_label_text') | |
| .filter(function(d){ return d.name == search_gene}) | |
| .select('text') | |
| .style('font-weight','bold'); | |
| // highlight row name | |
| d3.selectAll('.row_label_text') | |
| .filter(function(d){ return d.name == search_gene}) | |
| .select('rect') | |
| .style('opacity',1); | |
| // calculate the y panning required to center the found gene | |
| pan_dy = viz_height/2 - inst_y_pos; | |
| // use two translate method to control zooming | |
| // pan_x, pan_y, zoom | |
| two_translate_zoom(0, pan_dy, zoom_switch ); | |
| }; | |
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| { | |
| "row_nodes": [ | |
| { | |
| "sort": 25, | |
| "name": "CDK4" | |
| }, | |
| { | |
| "sort": 29, | |
| "name": "LMTK3" | |
| }, | |
| { | |
| "sort": 31, | |
| "name": "LRRK2" | |
| }, | |
| { | |
| "sort": 6, | |
| "name": "UHMK1" | |
| }, | |
| { | |
| "sort": 23, | |
| "name": "EGFR" | |
| }, | |
| { | |
| "sort": 19, | |
| "name": "STK32A" | |
| }, | |
| { | |
| "sort": 26, | |
| "name": "NRK" | |
| }, | |
| { | |
| "sort": 16, | |
| "name": "ERBB2" | |
| }, | |
| { | |
| "sort": 7, | |
| "name": "ERBB4" | |
| }, | |
| { | |
| "sort": 18, | |
| "name": "AAK1" | |
| }, | |
| { | |
| "sort": 3, | |
| "name": "SRPK3" | |
| }, | |
| { | |
| "sort": 5, | |
| "name": "STK39" | |
| }, | |
| { | |
| "sort": 2, | |
| "name": "GRK4" | |
| }, | |
| { | |
| "sort": 24, | |
| "name": "TBK1" | |
| }, | |
| { | |
| "sort": 33, | |
| "name": "INSRR" | |
| }, | |
| { | |
| "sort": 15, | |
| "name": "IRAK1" | |
| }, | |
| { | |
| "sort": 20, | |
| "name": "KDR" | |
| }, | |
| { | |
| "sort": 35, | |
| "name": "NPR1" | |
| }, | |
| { | |
| "sort": 27, | |
| "name": "PAK3" | |
| }, | |
| { | |
| "sort": 11, | |
| "name": "PDGFRA" | |
| }, | |
| { | |
| "sort": 34, | |
| "name": "PDK4" | |
| }, | |
| { | |
| "sort": 8, | |
| "name": "ULK4" | |
| }, | |
| { | |
| "sort": 30, | |
| "name": "PRKCE" | |
| }, | |
| { | |
| "sort": 0, | |
| "name": "PRKG2" | |
| }, | |
| { | |
| "sort": 36, | |
| "name": "MAPK4" | |
| }, | |
| { | |
| "sort": 12, | |
| "name": "MAPK11" | |
| }, | |
| { | |
| "sort": 21, | |
| "name": "STK31" | |
| }, | |
| { | |
| "sort": 37, | |
| "name": "GRK1" | |
| }, | |
| { | |
| "sort": 17, | |
| "name": "ROS1" | |
| }, | |
| { | |
| "sort": 22, | |
| "name": "MAP2K4" | |
| }, | |
| { | |
| "sort": 28, | |
| "name": "SRC" | |
| }, | |
| { | |
| "sort": 13, | |
| "name": "TGFBR1" | |
| }, | |
| { | |
| "sort": 4, | |
| "name": "CAMK2B" | |
| }, | |
| { | |
| "sort": 14, | |
| "name": "STK24" | |
| }, | |
| { | |
| "sort": 1, | |
| "name": "DCLK3" | |
| }, | |
| { | |
| "sort": 32, | |
| "name": "LATS1" | |
| }, | |
| { | |
| "sort": 10, | |
| "name": "NEK9" | |
| }, | |
| { | |
| "sort": 9, | |
| "name": "MYLK3" | |
| } | |
| ], | |
| "col_nodes": [ | |
| { | |
| "sort": 2, | |
| "name": "Cell-A" | |
| }, | |
| { | |
| "sort": 13, | |
| "name": "Cell-B" | |
| }, | |
| { | |
| "sort": 15, | |
| "name": "Cell-C" | |
| }, | |
| { | |
| "sort": 24, | |
| "name": "Cell-D" | |
| }, | |
| { | |
| "sort": 21, | |
| "name": "Cell-E" | |
| }, | |
| { | |
| "sort": 12, | |
| "name": "Cell-F" | |
| }, | |
| { | |
| "sort": 16, | |
| "name": "Cell-G" | |
| }, | |
| { | |
| "sort": 22, | |
| "name": "Cell-H" | |
| }, | |
| { | |
| "sort": 1, | |
| "name": "Cell-I" | |
| }, | |
| { | |
| "sort": 25, | |
| "name": "Cell-J" | |
| }, | |
| { | |
| "sort": 9, | |
| "name": "Cell-K" | |
| }, | |
| { | |
| "sort": 6, | |
| "name": "Cell-L" | |
| }, | |
| { | |
| "sort": 7, | |
| "name": "Cell-LM" | |
| }, | |
| { | |
| "sort": 4, | |
| "name": "Cell-N" | |
| }, | |
| { | |
| "sort": 20, | |
| "name": "Cell-O" | |
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| { | |
| "sort": 8, | |
| "name": "Cell-P" | |
| }, | |
| { | |
| "sort": 26, | |
| "name": "Cell-Q" | |
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| { | |
| "sort": 5, | |
| "name": "Cell-R" | |
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| { | |
| "sort": 18, | |
| "name": "Cell-S" | |
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| { | |
| "sort": 19, | |
| "name": "Cell-T" | |
| }, | |
| { | |
| "sort": 0, | |
| "name": "Cell-U" | |
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| "sort": 27, | |
| "name": "Cell-V" | |
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| "sort": 10, | |
| "name": "Cell-W" | |
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| { | |
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| "name": "Cell-X" | |
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| "name": "Cell-Y" | |
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| { | |
| "sort": 3, | |
| "name": "Cell-Z" | |
| }, | |
| { | |
| "sort": 14, | |
| "name": "Cell-Alpha" | |
| }, | |
| { | |
| "sort": 11, | |
| "name": "Cell-Beta" | |
| }, | |
| { | |
| "sort": 28, | |
| "name": "Cell-Gamma" | |
| } | |
| ], | |
| "links": [ | |
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| "value": -0.79280357071994445 | |
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| "value": 0.5276871273173751 | |
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| "value": 0.00062253607658903766 | |
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| "value": 0.35672259362868541 | |
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| "value": 0.93328608848913241 | |
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| "value": -0.13172853843578483 | |
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| "value": 0.80845194436217926 | |
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| "value": 1.1496185020456025 | |
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| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta http-equiv="X-UA-Compatible" content="IE=edge"> | |
| <meta name="viewport" content="width=device-width, initial-scale=1"> | |
| <meta name="description" content=""> | |
| <meta name="author" content=""> | |
| <title>D3 Clustergram</title> | |
| <!-- Bootstrap Core CSS --> | |
| <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"> | |
| <link rel="stylesheet" href="//code.jquery.com/ui/1.11.4/themes/smoothness/jquery-ui.css"> | |
| <link rel="stylesheet" href="custom.css"> | |
| </head> | |
| <body> | |
| <div id="wrapper" class='toggled'> | |
| <!-- Page Content --> | |
| <div id="page-content-wrapper"> | |
| <!-- Initial Content --> | |
| <div id='main_container'> | |
| <!-- this row is required, -fluid causes problems --> | |
| <div class="row" > | |
| <div class="col-lg-12"> | |
| <!-- visualization --> | |
| <div id='viz_container'> | |
| <div class='row'> | |
| <div id='clust_instruct_container' > | |
| <h1 id='viz_website_title'>D3 Clustergram</h1> | |
| <div id='viz_gmt_labels'></div> | |
| <div id='title_viz_instruct_text'>About:</div> | |
| <div class='viz_instruct_text'> This clustergram visualizes the example network located in static/networks/example_network.json. Zoom into the clustergram by scrolling. Double-click to reset zoom. Click on rows and columns to reorder. Search for a gene to zoom into the matrix. </div> | |
| <!-- input box for gene search --> | |
| <div id='gene_search_container' class='row'> | |
| <input id='gene_search_box' type="text" class="form-control" placeholder="Input Gene" aria-describedby="sizing-addon2"> | |
| <div id='gene_search_button' class="btn-group" data-toggle="buttons" > | |
| <label id='gene_search_submit' class="btn btn-primary active " onclick="find_gene_in_clust();"> | |
| <input type="radio" name="options" id="" autocomplete="off" checked > Search | |
| </label> | |
| </div> | |
| </div> | |
| <div id='toggle_order' class="btn-group" data-toggle="buttons" > | |
| <label class="btn btn-primary active prot_class" onclick="reorder_clust_rank('clust');"> | |
| <input type="radio" name="options" id="clust_button" autocomplete="off" checked > Cluster | |
| </label> | |
| <label class="btn btn-primary prot_class" onclick="reorder_clust_rank('rank');"> | |
| <input type="radio" name="options" id="rank_button" autocomplete="off" > Rank | |
| </label> | |
| </div> | |
| </div> | |
| </div> | |
| <div id='clustergram_container' > | |
| <div id='col_title'>Columns</div> | |
| <div id='clust_and_row_container'> | |
| <div id='row_title'>Rows</div> | |
| <div id='svg_div'></div> | |
| </div> | |
| </div> | |
| </div> | |
| </div> | |
| <!-- end visualization --> | |
| </div> | |
| </div> <!-- end row --> | |
| </div> | |
| </div> | |
| <!-- /#page-content-wrapper --> | |
| </div> | |
| <!-- /#wrapper --> | |
| <script src="//code.jquery.com/jquery-1.11.3.min.js"></script> | |
| <script src="//code.jquery.com/ui/1.11.4/jquery-ui.js"></script> | |
| <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script> | |
| <script src='d3_clustergram.js'></script> | |
| </body> | |
| </html> |
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