46121575bd78653f4443e6a4cbde0af6bb3f674c
ceisenhart
Wed Jan 13 13:26:30 2016 -0800
Heavy refactoring to the .html output, now all javascript is in the file d3.dendrograms.js, refs# 16216
diff --git src/hg/expMatrixToJson/expMatrixToJson.c src/hg/expMatrixToJson/expMatrixToJson.c
index 0bed5b1..742feff 100644
--- src/hg/expMatrixToJson/expMatrixToJson.c
+++ src/hg/expMatrixToJson/expMatrixToJson.c
@@ -7,31 +7,31 @@
#include "memalloc.h"
#include "jksql.h"
#include "expData.h"
#include "sqlList.h"
#include "hacTree.h"
#include "rainbow.h"
boolean clCSV = FALSE; // Converts the comma separated matrix into a tab based file.
boolean clMultiThreads = FALSE; // Allows the user to run the program with multiple threads, default is off.
int clThreads = 10; // The number of threads to run with the multiThreads option
int clMemLim = 4; // The amount of memeory the program can use, read in Gigabytes.
float clLongest = 0; // Used to normalize link distances in rlinkJson.
char* clDescFile = NULL; // The user can provide a description file
char* clAttributeTable = NULL; // The user can provide an attributes table... this may get removed soon.
int nodeCount; //The number of nodes.
-
+int internalNodes = 0;
void usage()
/* Explain usage and exit. */
{
errAbort(
"expMatrixToJson - Takes in an expression matrix and outputs a binary tree clustering the data.\n"
" The tree is output as a .json file, a .html file is generated to view the \n"
" tree. The files are named using the output argument (ex output.json, output.html).\n"
"usage:\n"
" expMatrixToJson [options] matrix output\n"
"options:\n"
" -multiThreads The program will run on multiple threads. \n"
" -CSV The input matrix is in .csv format. \n"
" -threads=int Sets the thread count for the multiThreads option, default is 10 \n"
" -memLim=int Sets the amount of memeory the program can use before aborting. The default is 4G. \n"
" -verbose=2 Show basic run stats. \n"
@@ -168,70 +168,71 @@
}
static void rPrintHierarchicalJson(FILE *f, struct hacTree *tree, int level, double distance)
/* Recursively prints out the elements of the hierarchical .json file. */
{
struct bioExpVector *bio = (struct bioExpVector *)tree->itemOrCluster;
char *tissue = bio->name;
struct rgbColor colors = bio->color;
if (tree->childDistance > clLongest)
/* In practice the first distance will be the longest, and is used for normalization. */
clLongest = tree->childDistance;
int i;
for (i = 0; i < level; i++)
fputc(' ', f); // correct spacing for .json format
+ // *****LEAVES*****
if (tree->left == NULL && tree->right == NULL)
// Print the leaf nodes
{
- if (bio->desc)
- fprintf(f, "{\"name\":\"%s\",\"length\":%f,\"distance\":\"%s\",\"colorGroup\":\"rgb(%i,%i,%i)\"}", tissue, (tree->parent->childDistance*tree->parent->childDistance) /1000, bio->desc, colors.r, colors.g, colors.b);
- else
- fprintf(f, "{\"name\":\"%s\",\"length\":%f,\"distance\":\"%s\",\"colorGroup\":\"rgb(%i,%i,%i)\"}", tissue, tree->parent->childDistance, " ", colors.r, colors.g, colors.b);
+ fprintf(f, "{\"name\":\"%s\",\"kids\":\"0\",\"length\":\"%f\",\"colorGroup\":\"rgb(%i,%i,%i)\"}",
+ tissue, tree->parent->childDistance, colors.r, colors.g, colors.b);
return;
}
else if (tree->left == NULL || tree->right == NULL)
errAbort("\nHow did we get a node with one NULL kid??");
-// Prints out the node object and opens a new children block.
for (i = 0; i < level + 1; i++)
fputc(' ', f);
distance = tree->childDistance/clLongest;
-double temp = 0;
+ double length = 0;
if (tree->parent != NULL)
{
- temp = tree->parent->childDistance;
+ length = tree->parent->childDistance;
}
-fprintf(f, "{\"name\": \" \", \"longestDistance\":\"%f\", \"tpmDistance\": \"%f\", \"length\": %f, \"colorGroup\": \"rgb(%i,"
- "%i,%i)\",",clLongest,tree->childDistance, temp*temp/1000, colors.r,colors.g,colors.b);
+ // *****NODES*****
+ ++internalNodes;
+ fprintf(f, "{\"name\":\" \", \"number\":\"%i\", \"kids\":\"%i\", \"tpmDistance\": \"%f\", \"length\": \"%f\", \"colorGroup\": \"rgb(%i,"
+ "%i,%i)\",",internalNodes, bio->children , tree->childDistance, length, colors.r,colors.g,colors.b);
if (distance != distance) distance = 0;
-//fprintf(f, "\"%s\"%s \"%f\"%s\n", "distance", ":", 100*distance, ",");
struct rgbColor wTB;
struct rgbColor wTBsqrt;
struct rgbColor wTBquad;
if (distance == 0) {
wTB = whiteToBlackRainbowAtPos(0);
wTBsqrt = whiteToBlackRainbowAtPos(0);
wTBquad = whiteToBlackRainbowAtPos(0);
}
else {
wTB = whiteToBlackRainbowAtPos(distance*.95);
wTBsqrt = whiteToBlackRainbowAtPos(sqrt(distance*.95));
wTBquad = whiteToBlackRainbowAtPos(sqrt(sqrt(distance*.95)));
}
-fprintf(f, "\"distance\": \"%f\", \"whiteToBlack\":\"rgb(%i,%i,%i)\", \"whiteTo", distance, wTB.r, wTB.g, wTB.b);
-fprintf(f, "BlackSqrt\":\"rgb(%i,%i,%i)\", \"whiteToBlackQuad\":\"rgb(%i,%i,%i)\",\n", wTBsqrt.r, wTBsqrt.g, wTBsqrt.b, wTBquad.r, wTBquad.g, wTBquad.b);
+ fprintf(f, "\"normalizedDistance\": \"%f\", \"whiteToBlack\":\"rgb(%i,%i,%i)\", \"whiteTo",
+ distance, wTB.r, wTB.g, wTB.b);
+ fprintf(f, "BlackSqrt\":\"rgb(%i,%i,%i)\", \"whiteToBlackQuad\":\"rgb(%i,%i,%i)\",\n",
+ wTBsqrt.r, wTBsqrt.g, wTBsqrt.b, wTBquad.r, wTBquad.g, wTBquad.b);
for (i = 0; i < level + 1; i++)
fputc(' ', f);
fprintf(f, "\"children\":[\n");
rPrintHierarchicalJson(f, tree->left, level+1, distance);
fputs(",\n", f);
rPrintHierarchicalJson(f, tree->right, level+1, distance);
fputc('\n', f);
// Closes the children block for node objects
for (i=0; i < level + 1; i++)
fputc(' ', f);
fputs("]\n", f);
for (i = 0; i < level; i++)
fputc(' ', f);
fputs("}", f);
}
@@ -331,33 +332,33 @@
{
double normalized = distance/total;
bio1->color = whiteToBlackRainbowAtPos(normalized);
firstLine = FALSE;
}
//if (distance != distance ) distance = 0 ;
//soFar += distance;
//double normalized = soFar/total;
double normalized = distance/total;
if (normalized * 100 >= .95) bio2->color = whiteToBlackRainbowAtPos(.95);
else bio2->color = whiteToBlackRainbowAtPos(normalized*100);
//bio2->color = saturatedRainbowAtPos(distance);
soFar += normalized;
}
/* Set first color to correspond to 0, since not set in above loop */
-//struct bioExpVector *bio = leafList->val;
+ struct bioExpVector *bio = leafList->val;
//bio->color = saturatedRainbowAtPos(0);
-//bio->color = whiteToBlackRainbowAtPos(0.0);
+ bio->color = whiteToBlackRainbowAtPos(.95);
}
void convertInput(char *expMatrix, char *descFile, bool csv)
/* Takes in a expression matrix and makes the inputs that this program will use.
* Namely a transposed table with the first column removed. Makes use of system calls
* to use cut, sed, kent utility rowsToCols, and paste (for descFile option). */
{
char cmd1[1024], cmd2[1024];
if (csv)
/* A sed one liner will convert comma separated values into a tab separated values*/
{
char cmd3[1024];
safef(cmd3, 1024, "sed -i 's/,/\\t/g' %s ",expMatrix);
verbose(2,"%s\n", cmd3);
mustSystem(cmd3);
@@ -384,242 +385,82 @@
else
{
safef(cmd2, 1024, "rowsToCols %s stdout | cut -f1 | sed \'1d\' > %s.cellNames", expMatrix, expMatrix);
verbose(2,"%s\n", cmd2);
mustSystem(cmd2);
}
}
void generateHtml(FILE *outputFile, int nameSize, char* jsonFile)
// Generates a new .html file for the dendrogram. Will do some size calculations as well.
{
char *pageName = cloneString(jsonFile);
chopSuffix(pageName);
int textSize = 12 - log(nodeCount);
int radius = 540 + 270*log10(nodeCount);
+ int width = 10 * nodeCount;
+ int height = 10 * nodeCount;
int labelLength = 10+nameSize*(15-textSize);
if (labelLength > 100) labelLength = 100;
-
fprintf(outputFile,"<!DOCTYPE html>\n");
-fprintf(outputFile,"<meta charset=\"utf-8\">\n");
-fprintf(outputFile,"<title>%s</title>\n", pageName);
-// CSS styles
-fprintf(outputFile,"<style>\n");
-fprintf(outputFile,"\t.node circle{fill: #ff f; stroke: steelblue; stroke-width: .25px;}\n");
-fprintf(outputFile,"\t.node{font: %ipx sans-serif;}\n", textSize);
-fprintf(outputFile,"\t.link{fill: none; stroke: #ccc; st roke-width: 1.5px;}\n");
-fprintf(outputFile,"\t.selectedLink{fill: none; stroke: #ccc; stroke-width: 3.0px;}\n");
-fprintf(outputFile,"\t.selected{fill: red;}\n");
-fprintf(outputFile,"\t.legend{font-size: 12px;}\n");
-fprintf(outputFile,"\trect{stroke-width: 2;}\n");
-fprintf(outputFile,"</style>\n");
-// Start body
-fprintf(outputFile,"<body>\n");
-// Scripts
+ fprintf(outputFile,"<head>\n");
+ fprintf(outputFile,"<title>New dendrogram tests</title>\n");
fprintf(outputFile,"<link rel=\"stylesheet\" href=\"http://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css\">\n");
fprintf(outputFile,"<script src=\"https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js\"></script>\n");
fprintf(outputFile,"<script src=\"http://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js\"></script>\n");
-fprintf(outputFile,"<script src=\"http://d3js.org/d3.v3.min.js\"></script>\n");
-// Adding dropdowns...
-fprintf(outputFile,"<div class = \"dropdown\">\n\t<ul style=\"list-style-type:none;display:inline-flex\">\n");
-// Inner nodes
-fprintf(outputFile,"\t\t<li class=\"dropdown\">\n");
-fprintf(outputFile,"\t\t\t<button class=\"btn btn-default dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\"> Inner nodes\n");
-fprintf(outputFile,"\t\t\t<span class=\"caret\"</span></button>\n");
-fprintf(outputFile,"\t\t\t<ul class=\"dropdown-menu\">\n");
-fprintf(outputFile,"\t\t\t\t<li><button onclick=\"nodeColors(0)\">tpm distance</button></li>\n");
-fprintf(outputFile,"\t\t\t\t<li><button onclick=\"nodeColors(1)\">sqrt tpm distance</button></li>\n");
-fprintf(outputFile,"\t\t\t\t<li><button onclick=\"nodeColors(2)\">quad rt tpm distance</button></li>\n");
-fprintf(outputFile,"\t\t\t</ul>\n\t\t</li>\n");
-// Inner leaves
-fprintf(outputFile,"\t\t<li class=\"dropdown\">\n");
-fprintf(outputFile,"\t\t\t<button class=\"btn btn-default dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\"> Inner leaves\n");
-fprintf(outputFile,"\t\t\t<span class=\"caret\"</span></button>\n");
-fprintf(outputFile,"\t\t\t<ul class=\"dropdown-menu\">\n");
-fprintf(outputFile,"<! Identifier >\n");
-fprintf(outputFile,"\t\t\t</ul>\n\t\t</li>\n");
-// Middle leaves
-fprintf(outputFile,"\t\t<li class=\"dropdown\">\n");
-fprintf(outputFile,"\t\t\t<button class=\"btn btn-default dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\"> Middle leaves\n");
-fprintf(outputFile,"\t\t\t<span class=\"caret\"</span></button>\n");
-fprintf(outputFile,"\t\t\t<ul class=\"dropdown-menu\">\n");
-fprintf(outputFile,"<! Identifier >\n");
-fprintf(outputFile,"\t\t\t</ul>\n\t\t</li>\n");
-// Outer leaves
-fprintf(outputFile,"\t\t<li class=\"dropdown\">\n");
-fprintf(outputFile,"\t\t\t<button class=\"btn btn-default dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\"> Outer leaves\n");
-fprintf(outputFile,"\t\t\t<span class=\"caret\"</span></button>\n");
-fprintf(outputFile,"\t\t\t<ul class=\"dropdown-menu\">\n");
-fprintf(outputFile,"<! Identifier >\n");
-fprintf(outputFile,"\t\t\t</ul>\n\t\t</li>\n");
-
-
-fprintf(outputFile,"\t</ul>\n</div>\n");
-fprintf(outputFile,"<div id=\"graph\"></div>\n");
-// Div the graph
+ fprintf(outputFile,"<script src=\"http://d3js.org/d3.v3.min.js\" type=\"text/javascript\"></script>\n");
+ fprintf(outputFile,"<script src=\"d3.dendrograms1.js\" type=\"text/javascript\"></script>\n");
+ fprintf(outputFile,"<div class = \"dropdown\">\n");
+ fprintf(outputFile," <div id = dropdown>\n");
+ fprintf(outputFile,"</div>\n");
fprintf(outputFile,"<script>\n");
-// Global variables and stuffs
-fprintf(outputFile,"\tvar radius= %i / 2;\n", radius);
-fprintf(outputFile,"\tvar cluster=d3.layout.cluster().size([360, radius - %i]);\n", labelLength);
-fprintf(outputFile,"\tvar colors=d3.scale.category20();\n");
-fprintf(outputFile,"\tvar diagonal=d3.svg.diagonal.radial().projection(function(d){return [d.y, d.x / 180 * Math.PI];});\n");
-fprintf(outputFile,"\tvar svg=d3.select(\"#graph\") .append(\"svg\") .attr(\"width\", 150 + (radius * 2) )\n");
-fprintf(outputFile,"\t\t.attr(\"height\", radius * 2) .append(\"g\") .attr(\"transform\",\n");
-fprintf(outputFile,"\t\t\"translate(\" + (radius + 150) + \",\" + radius + \")\");\n");
-fprintf(outputFile,"\tvar legendRectSize=20;\n");
-fprintf(outputFile,"\tvar legendSpacing=4;\n");
-fprintf(outputFile,"\tvar currentLegend=-1;\n");
-// Start D3 processing
-fprintf(outputFile,"\td3.json(\"%s\", function(error, root){\n", jsonFile);
-// Variable nodes
-fprintf(outputFile,"\t\tvar nodes=cluster.nodes(root);\n\n");
-// Variable link
-fprintf(outputFile,"\t\tvar link=svg.selectAll(\"path.link\")\n");
-fprintf(outputFile,"\t\t\t.data(cluster.links(nodes)).enter().append(\"path\")\n");
-fprintf(outputFile,"\t\t\t.attr(\"class\", \"link\").on(\"click\", function(){\n");
-fprintf(outputFile,"\t\t\td3.select(\".selectedLink\").classed(\"selectedLink\", false);\n");
-fprintf(outputFile,"\t\t\td3.select(this).classed(\"selectedLink\", true);}).attr(\"d\", diagonal);\n\n");
-// Graph variables!!! These are parsed by D3 and used to generate the actual dendrogram
-// Variable internalNodes
-fprintf(outputFile,"\t\tvar internalNodes = svg.selectAll(\"g.internalNode\")\n");
-fprintf(outputFile,"\t\t\t.data(nodes).enter().append(\"g\")\n");
-fprintf(outputFile,"\t\t\t.attr(\"class\", \"internalNode\").attr(\"transform\",\n");
-fprintf(outputFile,"\t\t\tfunction(d){\n");
-fprintf(outputFile,"\t\t\t\treturn \"rotate(\" + (d.x - 90) + \")translate(\" + d.y + \")\";});\n");
-fprintf(outputFile,"\t\t\t\tinternalNodes.append(\"circle\").attr(\"r\", function(d){\n");
-fprintf(outputFile,"\t\t\t\tif (d.name==\" \")\n");
-fprintf(outputFile,"\t\t\t\t{return 5;}\n"); //d.kids;}\n");
-fprintf(outputFile,"\t\t\t\telse{return 0;}})\n");
-fprintf(outputFile,"\t\t\t\t.style(\"fill\", function(d){\n");
-fprintf(outputFile,"\t\t\t\tif (d.name==\" \")\n");
-fprintf(outputFile,"\t\t\t\t{return d.whiteToBlack;}\n");
-fprintf(outputFile,"\t\t\t\telse{return \"none\";}})\n");
-fprintf(outputFile,"\t\t\t\t.style(\"stroke\", \"steelblue\")\n");
-fprintf(outputFile,"\t\t\t\t.style(\"stroke-width\", \"1.25px\");\n\n");
-// Variable innerLeaves
-fprintf(outputFile,"\t\tvar innerLeaves = svg.selectAll(\"g.innerLeaf\")\n");
-fprintf(outputFile,"\t\t\t.data(nodes).enter().append(\"g\")\n");
-fprintf(outputFile,"\t\t\t.attr(\"class\", \"innerLeaf\").attr(\"transform\",\n");
-fprintf(outputFile,"\t\t\tfunction(d){\n");
-fprintf(outputFile,"\t\t\t\treturn \"rotate(\" + (d.x - 90) + \")translate(\" + d.y + \")\";});\n");
-fprintf(outputFile,"\t\t\t\tinnerLeaves.append(\"circle\").attr(\"r\", function(d){\n");
-fprintf(outputFile,"\t\t\t\tif (d.name !==\" \")\n");
-fprintf(outputFile,"\t\t\t\t{return 5;}})\n");
-fprintf(outputFile,"\t\t\t\t.style(\"fill\", function(d){\n");
-fprintf(outputFile,"\t\t\t\tif (d.name !==\" \")\n");
-fprintf(outputFile,"\t\t\t\t{return \"d.whiteToBlack\";}\n");
-fprintf(outputFile,"\t\t\t\t})\n\n");
-// Variable middleLeaves
-fprintf(outputFile,"\t\tvar middleLeaves = svg.selectAll(\"g.middleLeaf\")\n");
-fprintf(outputFile,"\t\t\t.data(nodes).enter().append(\"g\")\n");
-fprintf(outputFile,"\t\t\t.attr(\"class\", \"middleLeaf\").attr(\"transform\",\n");
-fprintf(outputFile,"\t\t\tfunction(d){\n");
-fprintf(outputFile,"\t\t\t\treturn \"rotate(\" + (d.x - 90) + \")translate(\" + d.y + \")\";});\n");
-fprintf(outputFile,"\t\t\t\tmiddleLeaves.append(\"circle\").attr(\"r\", 5).style(\"fill\",\"none\");\n\n");
-// Variable outerLeaves
-fprintf(outputFile,"\t\tvar outerLeaves = svg.selectAll(\"g.outerLeaf\")\n");
-fprintf(outputFile,"\t\t\t.data(nodes).enter().append(\"g\")\n");
-fprintf(outputFile,"\t\t\t.attr(\"class\", \"outerLeaf\").attr(\"transform\",\n");
-fprintf(outputFile,"\t\t\tfunction(d){\n");
-fprintf(outputFile,"\t\t\t\treturn \"rotate(\" + (d.x - 90) + \")translate(\" + d.y + \")\";});\n");
-fprintf(outputFile,"\t\t\t\touterLeaves.append(\"circle\").attr(\"r\", 5).style(\"fill\",\"none\");\n\n");
-// Legend variables!!! These are parsed by D3 and used to generate the legends
-// Variable innerLegend
-fprintf(outputFile,"\t\t\tvar innerLegend=svg.selectAll('.innerLegend') .data(colors.domain()) .enter()\n");
-fprintf(outputFile,"\t\t\t.append('g') .attr('class', 'innerLegend')\n");
-fprintf(outputFile,"\t\t\t.attr('transform', \n");
-fprintf(outputFile,"\t\t\tfunction (d, i){\n");
-fprintf(outputFile,"\t\t\t\tvar height=legendRectSize + legendSpacing;\n");
-fprintf(outputFile,"\t\t\t\tvar offset=height * colors.domain().length / 2;\n");
-fprintf(outputFile,"\t\t\t\tvar horz=-2 * legendRectSize;\n");
-fprintf(outputFile,"\t\t\t\tvar vert=i * height - offset;\n");
-fprintf(outputFile,"\t\t\t\treturn 'translate(' + horz + ',' + vert + ')';}\n");
-fprintf(outputFile,"\t\t\t);\n");
-fprintf(outputFile,"\t\t\tinnerLegend.append('rect') .attr('width', legendRectSize) .attr('height', legendRectSize)\n");
-fprintf(outputFile,"\t\t\t.style('fill', colors) .style('stroke', colors);\n");
-fprintf(outputFile,"\t\t\tinnerLegend.append('text') .attr('x', legendRectSize + legendSpacing)\n");
-fprintf(outputFile,"\t\t\t.attr('y', legendRectSize - legendSpacing) .text(function (d){return d;});\n\n");
-// Variable middleLegend
-fprintf(outputFile,"\t\t\tvar middleLegend=svg.selectAll('.middleLegend') .data(colors.domain()) .enter()\n");
-fprintf(outputFile,"\t\t\t.append('g') .attr('class', 'middlerLegend')\n");
-fprintf(outputFile,"\t\t\t.attr('transform', \n");
-fprintf(outputFile,"\t\t\tfunction (d, i){\n");
-fprintf(outputFile,"\t\t\t\tvar height=legendRectSize + legendSpacing;\n");
-fprintf(outputFile,"\t\t\t\tvar offset=height * colors.domain().length / 2;\n");
-fprintf(outputFile,"\t\t\t\tvar horz=-2 * legendRectSize;\n");
-fprintf(outputFile,"\t\t\t\tvar vert=i * height - offset;\n");
-fprintf(outputFile,"\t\t\t\treturn 'translate(' + horz + ',' + vert + ')';}\n");
-fprintf(outputFile,"\t\t\t);\n");
-fprintf(outputFile,"\t\t\tmiddleLegend.append('rect') .attr('width', legendRectSize) .attr('height', legendRectSize)\n");
-fprintf(outputFile,"\t\t\t.style('fill', colors) .style('stroke', colors);\n");
-fprintf(outputFile,"\t\t\tmiddleLegend.append('text') .attr('x', legendRectSize + legendSpacing)\n");
-fprintf(outputFile,"\t\t\t.attr('y', legendRectSize - legendSpacing) .text(function (d){return d;});\n\n");
-// Variable outerLegend
-fprintf(outputFile,"\t\t\tvar outerLegend=svg.selectAll('.outerLegend') .data(colors.domain()) .enter()\n");
-fprintf(outputFile,"\t\t\t.append('g') .attr('class', 'outerLegend')\n");
-fprintf(outputFile,"\t\t\t.attr('transform', \n");
-fprintf(outputFile,"\t\t\tfunction (d, i){\n");
-fprintf(outputFile,"\t\t\t\tvar height=legendRectSize + legendSpacing;\n");
-fprintf(outputFile,"\t\t\t\tvar offset=height * colors.domain().length / 2;\n");
-fprintf(outputFile,"\t\t\t\tvar horz=-2 * legendRectSize;\n");
-fprintf(outputFile,"\t\t\t\tvar vert=i * height - offset;\n");
-fprintf(outputFile,"\t\t\t\treturn 'translate(' + horz + ',' + vert + ')';}\n");
-fprintf(outputFile,"\t\t\t);\n");
-fprintf(outputFile,"\t\t\touterLegend.append('rect') .attr('width', legendRectSize) .attr('height', legendRectSize)\n");
-fprintf(outputFile,"\t\t\t.style('fill', colors) .style('stroke', colors);\n");
-fprintf(outputFile,"\t\t\touterLegend.append('text') .attr('x', legendRectSize + legendSpacing)\n");
-fprintf(outputFile,"\t\t\t.attr('y', legendRectSize - legendSpacing) .text(function (d){return d;});\n\n");
-fprintf(outputFile,"\t\t\t});\n");
-// Function updateLegend
-fprintf(outputFile,"\tfunction updateLegend(val, layer, shift){\n");
-fprintf(outputFile,"\t\tvar legend=svg.selectAll('g.'+layer+'legend').data(val);\n");
-fprintf(outputFile,"\t\tlegend.enter() .append('g') .attr('class', 'legend') .attr('transform', function (d, i){\n");
-fprintf(outputFile,"\t\t\tvar height=legendRectSize + legendSpacing;\n");
-fprintf(outputFile,"\t\t\tvar offset=height *colors.domain().length / 2;\n");
-fprintf(outputFile,"\t\t\tvar horz=(-2 * legendRectSize) - radius - 75;\n");
-fprintf(outputFile,"\t\t\tvar vert=-(i * height - offset);\n");
-fprintf(outputFile,"\t\t\treturn 'translate(' + horz + ',' + vert + ')';});\n");
-fprintf(outputFile,"\t\tlegend.append('rect') .attr('width', legendRectSize) .attr('height', legendRectSize)\n");
-fprintf(outputFile,"\t\t.style('fill', colors) .style('stroke', colors);\n");
-fprintf(outputFile,"\t\tlegend.append('text') .attr('x', legendRectSize + legendSpacing)\n");
-fprintf(outputFile,"\t\t.attr('y', legendRectSize - legendSpacing) .text(function (d){return d;});}\n\n");
-// Function leafColors
-fprintf(outputFile,"\tfunction leafColors(val, layer, shift){\n");
-fprintf(outputFile,"\t\tvar node = svg.selectAll(\"g.\" + layer + \"Leaf\")\n");
-fprintf(outputFile,"\t\t.selectAll(\"circle\").style(\"fill\", function(d){\n");
-fprintf(outputFile,"\t\t\tif (d.name !== \" \"){\n");
-fprintf(outputFile,"\t\t\t\tif (val ===0) {return d3.rgb(d.colorGroup);}\n");
-fprintf(outputFile,"\t\t /* Identifier */\n");
-fprintf(outputFile,"\t\t\t}\n");
-fprintf(outputFile,"\t\t\t\telse{return 'none'}});\n");
-fprintf(outputFile,"\t\tvar legend=svg.selectAll('g.' + layer + 'Legend').remove();\n");
-fprintf(outputFile,"\t\tif (val >= 0) updateLegend(colors.domain(), layer);\n");
-fprintf(outputFile,"\t\tcolors=d3.scale.category20();}\n\n");
-// Function nodeColors
-fprintf(outputFile,"\tfunction nodeColors(val){\n");
-fprintf(outputFile,"\t\tvar node=svg.selectAll(\"g.internalNode\").selectAll(\"circle\")\n");
-fprintf(outputFile,"\t\t.style(\"fill\",function(d){\n");
-fprintf(outputFile,"\t\t\tif (d.name === \" \"){\n");
-fprintf(outputFile,"\t\t\t\tif (val==-1) return d3.rgb(d.colorGroup);\n");
-fprintf(outputFile,"\t\t\t\tif (val==0) return d3.rgb(d.whiteToBlack);\n");
-fprintf(outputFile,"\t\t\t\tif (val==1) return d3.rgb(d.whiteToBlackSqrt);\n");
-fprintf(outputFile,"\t\t\t\tif (val==2) return d3.rgb(d.whiteToBlackQuad);\n");
-fprintf(outputFile,"}});\n");
-fprintf(outputFile,"\t\t}\n");
+ fprintf(outputFile," function load() {\n");
+ fprintf(outputFile," var data;\n\n");
+ fprintf(outputFile," d3.json(\"testClustersWMeta.json\", function(error,json){\n");
+ fprintf(outputFile," if (error) return console.warn(error);\n");
+ fprintf(outputFile," data = json;\n");
+ fprintf(outputFile," d3.dendrogram.makeCartesianDendrogram('#phylogram', data, {\n");
+ fprintf(outputFile," width: %i,\n", width);
+ fprintf(outputFile," height: %i,\n", height);
+ fprintf(outputFile," });\n\n");
+ fprintf(outputFile," d3.dendrogram.makeRadialDendrogram('#dendrogram', data,{\n");
+ fprintf(outputFile," radius: %i,\n", radius);
+ fprintf(outputFile," });\n");
+ fprintf(outputFile," });\n");
+ fprintf(outputFile," }\n");
fprintf(outputFile,"</script>\n");
-fprintf(outputFile,"</body>");
+ fprintf(outputFile,"<style type=\"text/css\" media=\"screen\">\n");
+ fprintf(outputFile," body { font-family: \"Helvetica Neue\", Helvetica, sans-serif; }\n");
+ fprintf(outputFile," td { vertical-align: top; }\n");
+ fprintf(outputFile,"</style>\n");
+ fprintf(outputFile,"</head>\n");
+ fprintf(outputFile,"<body onload=\"load()\">\n");
+ fprintf(outputFile,"<table>\n");
+ fprintf(outputFile," <tr>\n");
+ fprintf(outputFile," <td>\n");
+ fprintf(outputFile," <h1>Phylogram</h2>\n");
+ fprintf(outputFile," <div id='phylogram'></div>\n");
+ fprintf(outputFile," </td>\n");
+ fprintf(outputFile," <td>\n");
+ fprintf(outputFile," <h1>Dendrogram</h1>\n");
+ fprintf(outputFile," <div id='dendrogram'></div>\n");
+ fprintf(outputFile," </td>\n");
+ fprintf(outputFile," </tr>\n");
+ fprintf(outputFile,"</table>\n");
+ fprintf(outputFile,"</body>\n");
+ fprintf(outputFile,"</html>\n");
carefulClose(&outputFile);
}
void expData(char *matrixFile, char *outDir, char *descFile)
/* Read matrix and names into a list of bioExpVectors, run hacTree to
* associate them, and write output. */
{
verbose(2,"Start binary clustering of the expression matrix by euclidean distance (expMatrixToJson).\n");
clock_t begin, end;
begin = clock();
convertInput(matrixFile, descFile, clCSV);
@@ -646,31 +487,30 @@
struct slRef *orderedList = getOrderedLeafList(clusters);
colorLeaves(orderedList);
printHierarchicalJson(f, clusters);
FILE *htmlF = mustOpen(catTwoStrings(outDir,".html"),"w");
generateHtml(htmlF,size,catTwoStrings(outDir,".json"));
// Remove temporary files
char cleanup[1024], cleanup2[1024];
safef(cleanup, 1024, "rm %s.cellNames", matrixFile);
safef(cleanup2, 1024, "rm %s.transposedMatrix", matrixFile);
mustSystem(cleanup);
mustSystem(cleanup2);
end = clock();
verbose(2,"%lld allocated at end. The program took %f seconds to complete.\n", (long long)carefulTotalAllocated(), (double)(end-begin)/CLOCKS_PER_SEC);
-
verbose(2,"Completed binary clustering of the expression matrix by euclidean distance (expMatrixToJson).\n");
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
clCSV = optionExists("CSV");
clMultiThreads = optionExists("multiThreads");
clThreads = optionInt("threads", clThreads);
clMemLim = optionInt("memLim", clMemLim);
clDescFile = optionVal("descFile", clDescFile);
if (argc != 3)
usage();
pushCarefulMemHandler(1L*1024*1024*1024*clMemLim);