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view_nice.php
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view_nice.php
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<?php
session_start();
include('bio_utils.php');
include('php_utils.php');
?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8"/>
<link rel="stylesheet" href="style.css"/>
<title>Viewing a job</title>
</head>
<body>
<?php include('top_bar.php'); ?>
<noscript>
It seems javascript isn't enabled. This website uses it for
many fuctionalities (some navigation buttons, sorting and so on),
so please enable javascript if you want to have full functionality !<br/>
This page in particular cannot yield good content with javascript disabled !
</noscript>
<?php
// Getting $job and $status
$params = _test2(get_GET_parameters(array('job')));
$job = $params['job'];
// Getting the sequences
$raw_input = _test2(fimo_get_input(session_id(), $job));
$input = format_sequence_into_sequences($raw_input);
// Getting the fimo output
$raw_output = _test2(fimo_get_raw_output(session_id(), $job));
// Formatting output for display
// We won't use the titles, though
$output = split_into_matrix($raw_output);
$titles = $output[0];
$data = array_slice($output, 1);
// The sequence names
$input_keys = array_keys($input);
?>
<fieldset id="nice_filters">
<legend>Filters</legend>
Score limit: <input type="text" id="text_score"><br/><br/>
p-value limit:
<select id="select_p-value">
<option value="0.001">10⁻⁴ (default)</option>
<option value="0.0001">10⁻⁵</option>
<option value="0.00001">10⁻⁶</option>
<option value="0.000001">10⁻⁷</option>
</select><br/>
<!-- q-value limit: -->
<select id="select_q-value" hidden=true>
<option value="1">No limit</option>
<option value="0.01">0.01</option>
<option value="0.001">0.001</option>
<option value="0.0001">0.0001</option>
</select><br/>
<button id="filter_button" onclick="filter_button_onclick()">Filter !</button>
</fieldset>
<fieldset id="nice_colours">
<legend>Colours</legend>
Colour according to
<select id="select_colour_method" onchange="change_colour_method()">
<option value="random">(random)</option>
<option value="score">score</option>
<option value="p-value">p-value</option>
<!-- <option value="q-value">q-value</option>-->
</select>
</fieldset>
<fieldset id="nice_other">
<legend>Other operations</legend>
Show only sequence
<select id="select_only_sequence" onchange="select_only_sequence()">
<option value="all">(all sequences)</option>
<?php
foreach ($input_keys as $key)
{
echo "<option value=\"$key\">$key</option>";
}
?>
</select><br/><br/>
Show only transcription factor
<select id="select_tfs" onchange="select_tfs()">
<option value="all">(all transcription factors)</option>
<?php
$tfs = array();
foreach ($data as $tf)
{
if (!in_array($tf[9], $tfs))
{
$tfs[] = $tf[9];
}
}
foreach ($tfs as $tf)
{
echo "<option value=\"$tf\">$tf</option>";
}
?>
</select><br/><br/>
<button onclick="get_raw_view()">Raw output</button>
</fieldset>
<?php
function cmp($a, $b)
{
return ($data[$a][6] < $data[$b][6])? -1 : 1;
}
$matches = get_matches($input_keys, $data);
// We display content (some is hidden) for the user
// and for us to process through javascript.
foreach ($input_keys as $key)
{
usort($matches[key], cmp);
$n_matched = sizeof($matches[$key]);
$patterns = array();
$starts = array();
$stops = array();
$strands = array();
$scores = array();
$pvalues = array();
$qvalues = array();
$sequences = array();
for ($i = 0; $i < $n_matched; $i++)
{
$patterns[] = $data[$matches[$key][$i]][9];
$starts[] = $data[$matches[$key][$i]][2];
$stops[] = $data[$matches[$key][$i]][3];
$strands[] = $data[$matches[$key][$i]][4];
$scores[] = $data[$matches[$key][$i]][5];
$pvalues[] = $data[$matches[$key][$i]][6];
$qvalues[] = $data[$matches[$key][$i]][7];
$sequences[] = $data[$matches[$key][$i]][8];
}
echo "<p id=\"p_$key\">\n$key:\n";
echo "<div hidden=\"true\">\n";
echo "<div id=\"input_$key\">" . $input[$key] . "</div>\n";
echo "<div id=\"patterns_$key\">" . implode($patterns, ',') . "</div>\n";
echo "<div id=\"starts_$key\">" . implode($starts, ',') . "</div>\n";
echo "<div id=\"stops_$key\">" . implode($stops, ',') . "</div>\n";
echo "<div id=\"strands_$key\">" . implode($strands, ',') . "</div>\n";
echo "<div id=\"scores_$key\">" . implode($scores, ',') . "</div>\n";
echo "<div id=\"p-values_$key\">" . implode($pvalues, ',') . "</div>\n";
echo "<div id=\"q-values_$key\">" . implode($qvalues, ',') . "</div>\n";
echo "<div id=\"sequences_$key\">" . implode($sequences, ',') . "</div>\n";
echo "</div>\n";
echo '<canvas id="canvas_' . $key . '"' . "></canvas>\n";
echo "<fieldset id=\"output_$key\">transcription factor:<br/>sequence:<br/>p-value:</fieldset>\n";
echo "</p>\n";
}
?>
<script type="text/javascript">
var g_job = "<?php echo $job; ?>";
var g_n_entries = <?php echo sizeof($input);?>;
var g_entries = ["<?php echo implode('", "', $input_keys);?>"];
var g_sequence_lengths = [];
var g_sequence_units = [];
var g_rects = [];
var g_width_factor = 0.8;
var g_width = window.innerWidth;
var g_x_offset_factor = 0.1;
var g_x_offset = window.innerWidth * g_x_offset_factor;
var g_canvas_width = g_width;
var g_canvas_default_height = 200;
var g_sequence_lines_y = [];
var g_sequence_line_width = g_width * g_width_factor;
var g_sequence_line_height = 5;
var g_sequence_text_height = 10;
var g_tfbox_height = 10;
var g_strand_text_x = 50;
var g_canvas_background_colour = "#FFFFFF";
var g_sequence_line_colour = "#000000";
var g_sequence_text_colour = "#000000";
var g_min_max_scores = [];
// name should be "input", "patterns", "starts", "stops" or "strands"
function get_sequence_data(id, divname)
{
var div = document.getElementById(divname + "_" + g_entries[id]);
return div.textContent;
}
function get_sequence_length(id)
{
var seq = get_sequence_data(id, "input");
return seq.length;
}
function draw_sequence_line(id, canvas, context)
{
var height = g_sequence_lines_y[id];
context.fillStyle = g_sequence_line_colour;
context.fillRect(g_x_offset, height, g_sequence_line_width, g_sequence_line_height);
}
function get_highest_power_of_10(n)
{
var i = 1;
while (n / i >= 1)
{
i *= 10;
}
return i / 10;
}
function draw_bp(id, canvas, context)
{
var height = g_sequence_lines_y[id];
var length = g_sequence_lengths[id];
var pow10 = get_highest_power_of_10(length);
// if length = 10xx, pow10 = 1000 ; we may want
// to draw a more detailed scale than 0 and 1000.
if (length - pow10 < pow10)
pow10 /= 10;
context.fillStyle = g_sequence_text_colour;
context.font = g_sequence_text_height + "px Arial";
var max = length / pow10;
var t;
for (var i = 0; i < max; i++)
{
t = i * pow10;
context.fillText(t, g_x_offset + t * g_sequence_units[id], height);
}
context.fillText("+ strand:", g_x_offset - g_strand_text_x, height/* - g_sequence_text_height*/);
context.fillText("- strand:", g_x_offset - g_strand_text_x, height + g_sequence_text_height + 3);
}
function gen_random_colour()
{
var colour = "#";
for (var i = 0; i < 6; i++)
{
colour += Math.floor(Math.random() * 16).toString(16);
}
return colour;
}
function p_inside(p, x, w)
{
return (x <= p && p <= x + w);
}
function ranges_intersect(r1, r2)
{
if (!(r1[6] && r2[6]))
{
return false;
}
else if (r1[5]*r2[5] < 0)
{
return false;
}
else if (p_inside(r1[0], r2[0], r2[2]) || p_inside(r2[0], r1[0], r1[2]))
{
return true;
}
else
{
return false;
}
}
function find_free_space(id, rects, drawn)
{
var n_drawn = drawn.length;
// Every rect which could intersect ;
// other strand rects are not neighbours
var neighbours = [];
for (var i = 0; i < n_drawn; i++)
{
if (ranges_intersect(rects[id], rects[drawn[i]]))
{
if (id != i)
{
neighbours.push(i);
}
}
}
var broke = true;
var n_neighbours = neighbours.length;
while (broke)
{
broke = false;
for (var i = 0; i < n_neighbours; i++)
{
if (rects[id][1] == rects[neighbours[i]][1])
{
rects[id][1] += g_tfbox_height;
broke = true;
break;
}
}
}
}
function calculate_rects(id, recalculate)
{
var starts = get_sequence_data(id, "starts").split(",");
var stops = get_sequence_data(id, "stops").split(",");
var strands = get_sequence_data(id, "strands").split(",");
var n_matched = starts.length;
var drawn = [];
// First pass ; y is not that important yet
for (var i = 0; i < n_matched; i++)
{
var dx = stops[i] - starts[i];
var x = g_sequence_units[id] * starts[i];
var y = 0;
var w = g_sequence_units[id] * dx;
var h = g_tfbox_height;
var colour = gen_random_colour();
var strand = (strands[i] == "+")? 1 : -1;
var shown = true;
if (recalculate)
{
var rect = g_rects[id][i];
g_rects[id][i] = [x, y, w, h, rect[4], strand, rect[6]];
}
else
{
g_rects[id][i] = [x, y, w, h, colour, strand, shown];
}
}
// Second pass: finding room for the y
for (var i = 0; i < n_matched; i++)
{
find_free_space(i, g_rects[id], drawn);
drawn.push(i);
}
// Third pass: correction of x (+offset),
// and y (according to strand)
for (var i = 0; i < n_matched; i++)
{
g_rects[id][i][0] += g_x_offset;
var strand = g_rects[id][i][5];
var y = strand * g_rects[id][i][1];
if (strand > 0)
{
y += g_tfbox_height + g_sequence_text_height - 3;
}
else
{
y -= g_sequence_line_height;
}
g_rects[id][i][1] = y;
}
}
function draw_tfboxes(id, canvas, context)
{
var n_matched = g_rects[id].length;
var y = g_sequence_lines_y[id];
for (var i = 0; i < n_matched; i++)
{
var rect = g_rects[id][i];
if (rect[6])
{
context.fillStyle = rect[4];
context.fillRect(rect[0], y - rect[1], rect[2], rect[3]);
}
}
}
function get_canvas_height(id)
{
var n_rects = g_rects[id].length;
var highest = 0;
var lowest = 0;
for (var i = 0; i < n_rects; i++)
{
if (g_rects[id][i][1] > highest)
{
highest = g_rects[id][i][1];
}
if (g_rects[id][i][1] < lowest)
{
lowest = g_rects[id][i][1];
}
}
return [highest - lowest + g_tfbox_height, highest];
}
function min(input)
{
return Math.min.apply(null, input);
}
function max(input)
{
return Math.max.apply(null, input);
}
function get_min_max(id)
{
var scores = get_sequence_data(id, "scores").split(",");
var pvalues = get_sequence_data(id, "p-values").split(",");
var qvalues = get_sequence_data(id, "q-values").split(",");
var ret = {};
// No good functional tools to do that in a short way... :(
var scores2 = [];
var pvalues2 = [];
var qvalues2 = [];
for (var i = 0; i < scores.length; i++)
{
if (g_rects[id][i][6])
{
scores2.push(scores[i]);
pvalues2.push(pvalues[i]);
qvalues2.push(qvalues[i]);
}
}
ret["score"] = [min(scores2), max(scores2)];
ret["p-value"] = [min(pvalues2), max(pvalues2)];
ret["q-value"] = [min(qvalues2), max(qvalues2)];
ret["score"][2] = ret["score"][1] - ret["score"][0];
ret["p-value"][2] = ret["p-value"][1] - ret["p-value"][0];
ret["q-value"][2] = ret["q-value"][1] - ret["q-value"][0];
return ret;
}
(function(){
for (var i = 0; i < g_n_entries; i++)
{
var canvas = document.getElementById("canvas_" + g_entries[i]);
var context = canvas.getContext("2d");
canvas.width = g_canvas_width;
canvas.height = g_canvas_default_height;
canvas.number = i;
canvas.onmousemove = canvas_mouse_move;
g_sequence_lengths[i] = get_sequence_length(i);
g_sequence_units[i] = g_sequence_line_width / g_sequence_lengths[i];
g_rects[i] = [];
calculate_rects(i, false);
height_highest = get_canvas_height(i);
canvas.height = height_highest[0];
g_sequence_lines_y[i] = height_highest[1];
g_min_max_scores[i] = get_min_max(i);
}
refresh_canvas();
})();
function refresh_canvas()
{
for (var i = 0; i < g_n_entries; i++)
{
var canvas = document.getElementById("canvas_" + g_entries[i]);
var context = canvas.getContext("2d");
context.fillStyle = g_canvas_background_colour;
context.fillRect(0, 0, canvas.width, canvas.height);
draw_sequence_line(i, canvas, context);
draw_bp(i, canvas, context);
draw_tfboxes(i, canvas, context);
}
}
function get_colour_from(rmask, gmask, bmask, intensity)
{
var ret = "#";
ret += ("00" + Math.floor(rmask*intensity).toString(16)).slice(-2);
ret += ("00" + Math.floor(gmask*intensity).toString(16)).slice(-2);
ret += ("00" + Math.floor(bmask*intensity).toString(16)).slice(-2);
return ret;
}
function get_colour_for(intensity)
{
/* Green to red gradient. */
var ret = "";
/* ret += ("00" + Math.floor(255*intensity).toString(16)).slice(-2);
ret += ("00" + Math.floor(255*(1-intensity)).toString(16)).slice(-2);
ret += "00";*/
/* Blue to yellow gradient. */
ret += ("00" + Math.floor(255*(1-intensity)).toString(16)).slice(-2);
ret += ret;
ret += ("00" + Math.floor(255*intensity).toString(16)).slice(-2);
/* Black to red gradient. */
/* ret += ("00" + Math.floor(255*intensity).toString(16)).slice(-2);
ret += "0000";*/
return "#" + ret;
}
function change_colour_method()
{
var select = document.getElementById("select_colour_method");
var method = select.value;
for (var i = 0; i < g_n_entries; i++)
{
var scores = get_sequence_data(i, "scores").split(",");
var pvalues = get_sequence_data(i, "p-values").split(",");
var qvalues = get_sequence_data(i, "q-values").split(",");
var n_matched = g_rects[i].length;
for (var j = 0; j < n_matched; j++)
{
switch (method)
{
case "random":
g_rects[i][j][4] = gen_random_colour();
break;
case "score":
var minimum = g_min_max_scores[i]["score"][0];
var normalised = (scores[j]-minimum)/g_min_max_scores[i]["score"][2];
g_rects[i][j][4] = get_colour_for(normalised);
break;
case "p-value":
var minimum = g_min_max_scores[i]["p-value"][0];
var normalised = (pvalues[j]-minimum)/g_min_max_scores[i]["p-value"][2];
g_rects[i][j][4] = get_colour_for(normalised);
break;
case "q-value":
var minimum = g_min_max_scores[i]["q-value"][0];
var normalised = (qvalues[j]-minimum)/g_min_max_scores[i]["q-value"][2];
g_rects[i][j][4] = get_colour_for(normalised);
break;
default:
break;
}
}
}
refresh_canvas();
}
function hide_entries_by(l_score, l_pvalue, l_qvalue)
{
if (l_score.length < 1)
{
l_score = -10000;
}
else
{
l_score = parseFloat(l_score);
}
for (var i = 0; i < g_n_entries; i++)
{
var scores = get_sequence_data(i, "scores").split(",");
var pvalues = get_sequence_data(i, "p-values").split(",");
var qvalues = get_sequence_data(i, "q-values").split(",");
var n_matched = g_rects[i].length;
for (var j = 0; j < n_matched; j++)
{
g_rects[i][j][6] = (scores[j] > l_score && pvalues[j] < l_pvalue/* && qvalues[j] < l_qvalue*/);
}
}
}
function filter_button_onclick()
{
var score = document.getElementById("text_score").value;
var pvalue = document.getElementById("select_p-value").value;
var qvalue = document.getElementById("select_q-value").value;
if (isNaN(score))
{
alert("Please enter a number in the 'Score limit:' field.");
return;
}
hide_entries_by(score, parseFloat(pvalue), parseFloat(qvalue));
for (var i = 0; i < g_n_entries; i++)
{
var canvas = document.getElementById("canvas_" + g_entries[i]);
calculate_rects(i, true);
height_highest = get_canvas_height(i);
canvas.height = height_highest[0];
g_sequence_lines_y[i] = height_highest[1];
g_min_max_scores[i] = get_min_max(i);
}
// The hidden entries may have been minima, so we
// use this method, which refreshes canvas anyway
change_colour_method();
}
function select_only_sequence()
{
var select = document.getElementById("select_only_sequence");
var sequence = select.value;
var ps = [];
var canvases = [];
var outputs = [];
for (var i = 0; i < g_n_entries; i++)
{
ps.push(document.getElementById("p_" + g_entries[i]));
canvases.push(document.getElementById("canvas_" + g_entries[i]));
outputs.push(document.getElementById("output_" + g_entries[i]));
}
if (sequence == "all")
{
for (var i = 0; i < g_n_entries; i++)
{
ps[i].hidden = false;
canvases[i].hidden = false;
outputs[i].hidden = false;
}
}
else
{
for (var i = 0; i < g_n_entries; i++)
{
ps[i].hidden = (sequence == g_entries[i])? false : true;
canvases[i].hidden = (sequence == g_entries[i])? false : true;
outputs[i].hidden = (sequence == g_entries[i])? false : true;
}
}
}
function hide_entries_by_name(name)
{
for (var i = 0; i < g_n_entries; i++)
{
var names = get_sequence_data(i, "patterns").split(",");
var n_matched = g_rects[i].length;
for (var j = 0; j < n_matched; j++)
{
g_rects[i][j][6] = (names[j] == name);
}
}
}
function show_all_entries_again()
{
for (var i = 0; i < g_n_entries; i++)
{
var n_matched = g_rects[i].length;
for (var j = 0; j < n_matched; j++)
{
g_rects[i][j][6] = true;
}
}
}
function select_tfs()
{
var select = document.getElementById("select_tfs");
var tf = select.value;
if (tf == "all")
{
show_all_entries_again();
}
else
{
hide_entries_by_name(select.value);
}
/* To avoid bugs : resetting the filters. */
var score = document.getElementById("text_score");
var pvalue = document.getElementById("select_p-value");
var qvalue = document.getElementById("select_q-value");
score.value = "";
pvalue.value = "1";
qvalue.value = "1";
for (var i = 0; i < g_n_entries; i++)
{
var canvas = document.getElementById("canvas_" + g_entries[i]);
calculate_rects(i, true);
height_highest = get_canvas_height(i);
canvas.height = height_highest[0];
g_sequence_lines_y[i] = height_highest[1];
g_min_max_scores[i] = get_min_max(i);
}
refresh_canvas();
}
function canvas_mouse_move(event)
{
var e = event || window.event;
var rect = e.target.getBoundingClientRect();
var x = e.clientX - rect.left;
var y = e.clientY - rect.top;
var id = e.target.number;
var output = document.getElementById("output_" + g_entries[id]);
var on = -1;
for (var i = 0; i < g_rects[id].length; i++)
{
rect = g_rects[id][i];
if (!rect[6])
{
continue;
}
if (p_inside(x, rect[0], rect[2]) && p_inside(y, g_sequence_lines_y[id] - rect[1], rect[3]))
{
on = i;
}
}
if (on > -1)
{
var names = get_sequence_data(id, "patterns").split(",");
var seqs = get_sequence_data(id, "sequences").split(",");
var pvalues = get_sequence_data(id, "p-values").split(",");
var content = "";
content += "transcription factor: " + names[on] + "<br/>";
content += "sequence: " + seqs[on] + "<br/>";
content += "p-value: " + pvalues[on];
output.innerHTML = content;
}
else
{
output.innerHTML = "transcription factor:<br/>sequence:<br/>p-value:";
}
}
function get_raw_view()
{
window.location = "http://<?php echo $LAB_ADDRESS; ?>/view_output.php?job=" + g_job;
}
</script>
</body>
</html>