From fb40bfa27aef7dd088bf2467d0845e8935444c4b Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 9 Oct 2015 22:07:25 +0000 Subject: Fixed correlations for phenotype datasets Fixed table for some expression dataset searches Added collection button to correlation page Added color gradient to correlation matrix --- wqflask/wqflask/correlation/show_corr_results.py | 140 +- .../static/new/javascript/create_corr_matrix.js | 16 + wqflask/wqflask/static/new/js_external/chroma.js | 2464 ++++++++++++++++++++ wqflask/wqflask/templates/correlation_matrix.html | 18 +- wqflask/wqflask/templates/correlation_page.html | 27 +- wqflask/wqflask/templates/search_result_page.html | 9 +- .../show_trait_calculate_correlations.html | 3 +- 7 files changed, 2599 insertions(+), 78 deletions(-) create mode 100644 wqflask/wqflask/static/new/js_external/chroma.js diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 63a7a555..af8bb2ab 100755 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -104,23 +104,28 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] - if start_vars['min_expr'] == "": - self.min_expr = 0 - else: - self.min_expr = float(start_vars['min_expr']) + if 'min_expr' in start_vars: + if start_vars['min_expr'] != "": + self.min_expr = float(start_vars['min_expr']) + else: + self.min_expr = None self.p_range_lower = float(start_vars['p_range_lower']) self.p_range_upper = float(start_vars['p_range_upper']) - self.min_location_chr = start_vars['min_loc_chr'] - self.max_location_chr = start_vars['max_loc_chr'] - if start_vars['min_loc_mb'].isdigit(): - self.min_location_mb = start_vars['min_loc_mb'] - else: - self.min_location_mb = 0 - if start_vars['max_loc_mb'].isdigit(): - self.max_location_mb = start_vars['max_loc_mb'] - else: - self.max_location_mb = 1000 - self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']] + + if ('min_loc_chr' in start_vars and + 'max_loc_chr' in start_vars and + 'min_loc_mb' in start_vars and + 'max_loc_mb' in start_vars): + + self.min_location_chr = start_vars['min_loc_chr'] + self.max_location_chr = start_vars['max_loc_chr'] + if start_vars['min_loc_mb'].isdigit(): + self.min_location_mb = start_vars['min_loc_mb'] + else: + self.min_location_mb = 0 + if start_vars['max_loc_mb'].isdigit(): + self.max_location_mb = start_vars['max_loc_mb'] + self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -178,56 +183,79 @@ class CorrelationResults(object): key=lambda t: -abs(t[1][0]))) - #ZS: Convert min/max chromosome to an int for the location range option - min_chr_as_int = 1 - max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): - if chr_info.name == self.min_location_chr: - min_chr_as_int = order_id - if chr_info.name == self.max_location_chr: - max_chr_as_int = order_id + if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": + #ZS: Convert min/max chromosome to an int for the location range option + min_chr_as_int = 1 + max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing + for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + if chr_info.name == self.min_location_chr: + min_chr_as_int = order_id + if chr_info.name == self.max_location_chr: + max_chr_as_int = order_id for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): print("trait name:", trait) trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True) - #ZS: Convert trait chromosome to an int for the location range option - chr_as_int = 0 - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): - if chr_info.name == trait_object.chr: - chr_as_int = order_id - - if (float(trait_object.mean) > self.min_expr and - float(self.correlation_data[trait][0]) > self.p_range_lower and - float(self.correlation_data[trait][0]) < self.p_range_upper and - chr_as_int >= min_chr_as_int and - chr_as_int <= max_chr_as_int): - - if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)): - continue - elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)): - continue - - (trait_object.sample_r, - trait_object.sample_p, - trait_object.num_overlap) = self.correlation_data[trait] + if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": + #ZS: Convert trait chromosome to an int for the location range option + chr_as_int = 0 + for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + if chr_info.name == trait_object.chr: + chr_as_int = order_id + + if (float(self.correlation_data[trait][0]) >= self.p_range_lower and + float(self.correlation_data[trait][0]) <= self.p_range_upper): + + if ((self.dataset.type == "ProbeSet" or self.dataset.type == "Geno") and + (self.min_expr != None and float(trait_object.mean) >= self.min_expr) and + chr_as_int >= min_chr_as_int and + chr_as_int <= max_chr_as_int) : + + + if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)): + continue + elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)): + continue + + (trait_object.sample_r, + trait_object.sample_p, + trait_object.num_overlap) = self.correlation_data[trait] + + #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef, + #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions) - #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef, - #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions) + # Set some sane defaults + trait_object.tissue_corr = 0 + trait_object.tissue_pvalue = 0 + trait_object.lit_corr = 0 + if self.corr_type == "tissue": + trait_object.tissue_corr = tissue_corr_data[trait][1] + trait_object.tissue_pvalue = tissue_corr_data[trait][2] + elif self.corr_type == "lit": + trait_object.lit_corr = lit_corr_data[trait][1] + self.correlation_results.append(trait_object) + else: + (trait_object.sample_r, + trait_object.sample_p, + trait_object.num_overlap) = self.correlation_data[trait] - # Set some sane defaults - trait_object.tissue_corr = 0 - trait_object.tissue_pvalue = 0 - trait_object.lit_corr = 0 - if self.corr_type == "tissue": - trait_object.tissue_corr = tissue_corr_data[trait][1] - trait_object.tissue_pvalue = tissue_corr_data[trait][2] - elif self.corr_type == "lit": - trait_object.lit_corr = lit_corr_data[trait][1] - self.correlation_results.append(trait_object) + #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef, + #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions) + + # Set some sane defaults + trait_object.tissue_corr = 0 + trait_object.tissue_pvalue = 0 + trait_object.lit_corr = 0 + if self.corr_type == "tissue": + trait_object.tissue_corr = tissue_corr_data[trait][1] + trait_object.tissue_pvalue = tissue_corr_data[trait][2] + elif self.corr_type == "lit": + trait_object.lit_corr = lit_corr_data[trait][1] + self.correlation_results.append(trait_object) self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species) - + if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": self.do_lit_correlation_for_trait_list() diff --git a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js index df84b85a..adb91295 100644 --- a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js +++ b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js @@ -42,3 +42,19 @@ get_data = function() { data.rows = js_data.rows; return data; }; + + +var neg_color_scale = chroma.scale(['#FF0000', 'white']).domain([-1, -0.4]); +var pos_color_scale = chroma.scale(['white', 'aqua']).domain([0.4, 1]) +$('.corr_cell').each( function () { + corr_value = parseFloat($(this).find('span.corr_value').text()) + if (corr_value >= 0.5){ + $(this).css('background-color', pos_color_scale(parseFloat(corr_value))) + } + else if (corr_value <= -0.5) { + $(this).css('background-color', neg_color_scale(parseFloat(corr_value))) + } + else { + $(this).css('background-color', 'white') + } +}); \ No newline at end of file diff --git a/wqflask/wqflask/static/new/js_external/chroma.js b/wqflask/wqflask/static/new/js_external/chroma.js new file mode 100644 index 00000000..0976056b --- /dev/null +++ b/wqflask/wqflask/static/new/js_external/chroma.js @@ -0,0 +1,2464 @@ +/** + * @license + * + * chroma.js - JavaScript library for color conversions + * + * Copyright (c) 2011-2015, Gregor Aisch + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: + * + * 1. Redistributions of source code must retain the above copyright notice, this + * list of conditions and the following disclaimer. + * + * 2. Redistributions in binary form must reproduce the above copyright notice, + * this list of conditions and the following disclaimer in the documentation + * and/or other materials provided with the distribution. + * + * 3. The name Gregor Aisch may not be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL GREGOR AISCH OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, + * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY + * OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ + +(function() { + var Color, DEG2RAD, LAB_CONSTANTS, PI, PITHIRD, RAD2DEG, TWOPI, _guess_formats, _guess_formats_sorted, _input, _interpolators, abs, atan2, bezier, blend, blend_f, brewer, burn, chroma, clip_rgb, cmyk2rgb, colors, cos, css2rgb, darken, dodge, each, floor, hex2rgb, hsi2rgb, hsl2css, hsl2rgb, hsv2rgb, interpolate, interpolate_hsx, interpolate_lab, interpolate_num, interpolate_rgb, lab2lch, lab2rgb, lab_xyz, lch2lab, lch2rgb, lighten, limit, log, luminance_x, m, max, multiply, normal, num2rgb, overlay, pow, rgb2cmyk, rgb2css, rgb2hex, rgb2hsi, rgb2hsl, rgb2hsv, rgb2lab, rgb2lch, rgb2luminance, rgb2num, rgb2temperature, rgb2xyz, rgb_xyz, rnd, root, round, screen, sin, sqrt, temperature2rgb, type, unpack, w3cx11, xyz_lab, xyz_rgb, + slice = [].slice; + + type = (function() { + + /* + for browser-safe type checking+ + ported from jQuery's $.type + */ + var classToType, len, name, o, ref; + classToType = {}; + ref = "Boolean Number String Function Array Date RegExp Undefined Null".split(" "); + for (o = 0, len = ref.length; o < len; o++) { + name = ref[o]; + classToType["[object " + name + "]"] = name.toLowerCase(); + } + return function(obj) { + var strType; + strType = Object.prototype.toString.call(obj); + return classToType[strType] || "object"; + }; + })(); + + limit = function(x, min, max) { + if (min == null) { + min = 0; + } + if (max == null) { + max = 1; + } + if (x < min) { + x = min; + } + if (x > max) { + x = max; + } + return x; + }; + + unpack = function(args) { + if (args.length >= 3) { + return [].slice.call(args); + } else { + return args[0]; + } + }; + + clip_rgb = function(rgb) { + var i; + for (i in rgb) { + if (i < 3) { + if (rgb[i] < 0) { + rgb[i] = 0; + } + if (rgb[i] > 255) { + rgb[i] = 255; + } + } else if (i === 3) { + if (rgb[i] < 0) { + rgb[i] = 0; + } + if (rgb[i] > 1) { + rgb[i] = 1; + } + } + } + return rgb; + }; + + PI = Math.PI, round = Math.round, cos = Math.cos, floor = Math.floor, pow = Math.pow, log = Math.log, sin = Math.sin, sqrt = Math.sqrt, atan2 = Math.atan2, max = Math.max, abs = Math.abs; + + TWOPI = PI * 2; + + PITHIRD = PI / 3; + + DEG2RAD = PI / 180; + + RAD2DEG = 180 / PI; + + chroma = function() { + if (arguments[0] instanceof Color) { + return arguments[0]; + } + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, arguments, function(){}); + }; + + _interpolators = []; + + if ((typeof module !== "undefined" && module !== null) && (module.exports != null)) { + module.exports = chroma; + } + + if (typeof define === 'function' && define.amd) { + define([], function() { + return chroma; + }); + } else { + root = typeof exports !== "undefined" && exports !== null ? exports : this; + root.chroma = chroma; + } + + chroma.version = '1.1.1'; + + + /** + chroma.js + + Copyright (c) 2011-2013, Gregor Aisch + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + + * The name Gregor Aisch may not be used to endorse or promote products + derived from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL GREGOR AISCH OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, + INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY + OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + @source: https://github.com/gka/chroma.js + */ + + _input = {}; + + _guess_formats = []; + + _guess_formats_sorted = false; + + Color = (function() { + function Color() { + var arg, args, chk, len, len1, me, mode, o, w; + me = this; + args = []; + for (o = 0, len = arguments.length; o < len; o++) { + arg = arguments[o]; + if (arg != null) { + args.push(arg); + } + } + mode = args[args.length - 1]; + if (_input[mode] != null) { + me._rgb = clip_rgb(_input[mode](unpack(args.slice(0, -1)))); + } else { + if (!_guess_formats_sorted) { + _guess_formats = _guess_formats.sort(function(a, b) { + return b.p - a.p; + }); + _guess_formats_sorted = true; + } + for (w = 0, len1 = _guess_formats.length; w < len1; w++) { + chk = _guess_formats[w]; + mode = chk.test.apply(chk, args); + if (mode) { + break; + } + } + if (mode) { + me._rgb = clip_rgb(_input[mode].apply(_input, args)); + } + } + if (me._rgb == null) { + console.warn('unknown format: ' + args); + } + if (me._rgb == null) { + me._rgb = [0, 0, 0]; + } + if (me._rgb.length === 3) { + me._rgb.push(1); + } + } + + Color.prototype.alpha = function(alpha) { + if (arguments.length) { + this._rgb[3] = alpha; + return this; + } + return this._rgb[3]; + }; + + Color.prototype.toString = function() { + return this.name(); + }; + + return Color; + + })(); + + chroma._input = _input; + + + /** + ColorBrewer colors for chroma.js + + Copyright (c) 2002 Cynthia Brewer, Mark Harrower, and The + Pennsylvania State University. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software distributed + under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR + CONDITIONS OF ANY KIND, either express or implied. See the License for the + specific language governing permissions and limitations under the License. + + @preserve + */ + + chroma.brewer = brewer = { + OrRd: ['#fff7ec', '#fee8c8', '#fdd49e', '#fdbb84', '#fc8d59', '#ef6548', '#d7301f', '#b30000', '#7f0000'], + PuBu: ['#fff7fb', '#ece7f2', '#d0d1e6', '#a6bddb', '#74a9cf', '#3690c0', '#0570b0', '#045a8d', '#023858'], + BuPu: ['#f7fcfd', '#e0ecf4', '#bfd3e6', '#9ebcda', '#8c96c6', '#8c6bb1', '#88419d', '#810f7c', '#4d004b'], + Oranges: ['#fff5eb', '#fee6ce', '#fdd0a2', '#fdae6b', '#fd8d3c', '#f16913', '#d94801', '#a63603', '#7f2704'], + BuGn: ['#f7fcfd', '#e5f5f9', '#ccece6', '#99d8c9', '#66c2a4', '#41ae76', '#238b45', '#006d2c', '#00441b'], + YlOrBr: ['#ffffe5', '#fff7bc', '#fee391', '#fec44f', '#fe9929', '#ec7014', '#cc4c02', '#993404', '#662506'], + YlGn: ['#ffffe5', '#f7fcb9', '#d9f0a3', '#addd8e', '#78c679', '#41ab5d', '#238443', '#006837', '#004529'], + Reds: ['#fff5f0', '#fee0d2', '#fcbba1', '#fc9272', '#fb6a4a', '#ef3b2c', '#cb181d', '#a50f15', '#67000d'], + RdPu: ['#fff7f3', '#fde0dd', '#fcc5c0', '#fa9fb5', '#f768a1', '#dd3497', '#ae017e', '#7a0177', '#49006a'], + Greens: ['#f7fcf5', '#e5f5e0', '#c7e9c0', '#a1d99b', '#74c476', '#41ab5d', '#238b45', '#006d2c', '#00441b'], + YlGnBu: ['#ffffd9', '#edf8b1', '#c7e9b4', '#7fcdbb', '#41b6c4', '#1d91c0', '#225ea8', '#253494', '#081d58'], + Purples: ['#fcfbfd', '#efedf5', '#dadaeb', '#bcbddc', '#9e9ac8', '#807dba', '#6a51a3', '#54278f', '#3f007d'], + GnBu: ['#f7fcf0', '#e0f3db', '#ccebc5', '#a8ddb5', '#7bccc4', '#4eb3d3', '#2b8cbe', '#0868ac', '#084081'], + Greys: ['#ffffff', '#f0f0f0', '#d9d9d9', '#bdbdbd', '#969696', '#737373', '#525252', '#252525', '#000000'], + YlOrRd: ['#ffffcc', '#ffeda0', '#fed976', '#feb24c', '#fd8d3c', '#fc4e2a', '#e31a1c', '#bd0026', '#800026'], + PuRd: ['#f7f4f9', '#e7e1ef', '#d4b9da', '#c994c7', '#df65b0', '#e7298a', '#ce1256', '#980043', '#67001f'], + Blues: ['#f7fbff', '#deebf7', '#c6dbef', '#9ecae1', '#6baed6', '#4292c6', '#2171b5', '#08519c', '#08306b'], + PuBuGn: ['#fff7fb', '#ece2f0', '#d0d1e6', '#a6bddb', '#67a9cf', '#3690c0', '#02818a', '#016c59', '#014636'], + Spectral: ['#9e0142', '#d53e4f', '#f46d43', '#fdae61', '#fee08b', '#ffffbf', '#e6f598', '#abdda4', '#66c2a5', '#3288bd', '#5e4fa2'], + RdYlGn: ['#a50026', '#d73027', '#f46d43', '#fdae61', '#fee08b', '#ffffbf', '#d9ef8b', '#a6d96a', '#66bd63', '#1a9850', '#006837'], + RdBu: ['#67001f', '#b2182b', '#d6604d', '#f4a582', '#fddbc7', '#f7f7f7', '#d1e5f0', '#92c5de', '#4393c3', '#2166ac', '#053061'], + PiYG: ['#8e0152', '#c51b7d', '#de77ae', '#f1b6da', '#fde0ef', '#f7f7f7', '#e6f5d0', '#b8e186', '#7fbc41', '#4d9221', '#276419'], + PRGn: ['#40004b', '#762a83', '#9970ab', '#c2a5cf', '#e7d4e8', '#f7f7f7', '#d9f0d3', '#a6dba0', '#5aae61', '#1b7837', '#00441b'], + RdYlBu: ['#a50026', '#d73027', '#f46d43', '#fdae61', '#fee090', '#ffffbf', '#e0f3f8', '#abd9e9', '#74add1', '#4575b4', '#313695'], + BrBG: ['#543005', '#8c510a', '#bf812d', '#dfc27d', '#f6e8c3', '#f5f5f5', '#c7eae5', '#80cdc1', '#35978f', '#01665e', '#003c30'], + RdGy: ['#67001f', '#b2182b', '#d6604d', '#f4a582', '#fddbc7', '#ffffff', '#e0e0e0', '#bababa', '#878787', '#4d4d4d', '#1a1a1a'], + PuOr: ['#7f3b08', '#b35806', '#e08214', '#fdb863', '#fee0b6', '#f7f7f7', '#d8daeb', '#b2abd2', '#8073ac', '#542788', '#2d004b'], + Set2: ['#66c2a5', '#fc8d62', '#8da0cb', '#e78ac3', '#a6d854', '#ffd92f', '#e5c494', '#b3b3b3'], + Accent: ['#7fc97f', '#beaed4', '#fdc086', '#ffff99', '#386cb0', '#f0027f', '#bf5b17', '#666666'], + Set1: ['#e41a1c', '#377eb8', '#4daf4a', '#984ea3', '#ff7f00', '#ffff33', '#a65628', '#f781bf', '#999999'], + Set3: ['#8dd3c7', '#ffffb3', '#bebada', '#fb8072', '#80b1d3', '#fdb462', '#b3de69', '#fccde5', '#d9d9d9', '#bc80bd', '#ccebc5', '#ffed6f'], + Dark2: ['#1b9e77', '#d95f02', '#7570b3', '#e7298a', '#66a61e', '#e6ab02', '#a6761d', '#666666'], + Paired: ['#a6cee3', '#1f78b4', '#b2df8a', '#33a02c', '#fb9a99', '#e31a1c', '#fdbf6f', '#ff7f00', '#cab2d6', '#6a3d9a', '#ffff99', '#b15928'], + Pastel2: ['#b3e2cd', '#fdcdac', '#cbd5e8', '#f4cae4', '#e6f5c9', '#fff2ae', '#f1e2cc', '#cccccc'], + Pastel1: ['#fbb4ae', '#b3cde3', '#ccebc5', '#decbe4', '#fed9a6', '#ffffcc', '#e5d8bd', '#fddaec', '#f2f2f2'] + }; + + + /** + X11 color names + + http://www.w3.org/TR/css3-color/#svg-color + */ + + w3cx11 = { + indigo: "#4b0082", + gold: "#ffd700", + hotpink: "#ff69b4", + firebrick: "#b22222", + indianred: "#cd5c5c", + yellow: "#ffff00", + mistyrose: "#ffe4e1", + darkolivegreen: "#556b2f", + olive: "#808000", + darkseagreen: "#8fbc8f", + pink: "#ffc0cb", + tomato: "#ff6347", + lightcoral: "#f08080", + orangered: "#ff4500", + navajowhite: "#ffdead", + lime: "#00ff00", + palegreen: "#98fb98", + darkslategrey: "#2f4f4f", + greenyellow: "#adff2f", + burlywood: "#deb887", + seashell: "#fff5ee", + mediumspringgreen: "#00fa9a", + fuchsia: "#ff00ff", + papayawhip: "#ffefd5", + blanchedalmond: "#ffebcd", + chartreuse: "#7fff00", + dimgray: "#696969", + black: "#000000", + peachpuff: "#ffdab9", + springgreen: "#00ff7f", + aquamarine: "#7fffd4", + white: "#ffffff", + orange: "#ffa500", + lightsalmon: "#ffa07a", + darkslategray: "#2f4f4f", + brown: "#a52a2a", + ivory: "#fffff0", + dodgerblue: "#1e90ff", + peru: "#cd853f", + lawngreen: "#7cfc00", + chocolate: "#d2691e", + crimson: "#dc143c", + forestgreen: "#228b22", + darkgrey: "#a9a9a9", + lightseagreen: "#20b2aa", + cyan: "#00ffff", + mintcream: "#f5fffa", + silver: "#c0c0c0", + antiquewhite: "#faebd7", + mediumorchid: "#ba55d3", + skyblue: "#87ceeb", + gray: "#808080", + darkturquoise: "#00ced1", + goldenrod: "#daa520", + darkgreen: "#006400", + floralwhite: "#fffaf0", + darkviolet: "#9400d3", + darkgray: "#a9a9a9", + moccasin: "#ffe4b5", + saddlebrown: "#8b4513", + grey: "#808080", + darkslateblue: "#483d8b", + lightskyblue: "#87cefa", + lightpink: "#ffb6c1", + mediumvioletred: "#c71585", + slategrey: "#708090", + red: "#ff0000", + deeppink: "#ff1493", + limegreen: "#32cd32", + darkmagenta: "#8b008b", + palegoldenrod: "#eee8aa", + plum: "#dda0dd", + turquoise: "#40e0d0", + lightgrey: "#d3d3d3", + lightgoldenrodyellow: "#fafad2", + darkgoldenrod: "#b8860b", + lavender: "#e6e6fa", + maroon: "#800000", + yellowgreen: "#9acd32", + sandybrown: "#f4a460", + thistle: "#d8bfd8", + violet: "#ee82ee", + navy: "#000080", + magenta: "#ff00ff", + dimgrey: "#696969", + tan: "#d2b48c", + rosybrown: "#bc8f8f", + olivedrab: "#6b8e23", + blue: "#0000ff", + lightblue: "#add8e6", + ghostwhite: "#f8f8ff", + honeydew: "#f0fff0", + cornflowerblue: "#6495ed", + slateblue: "#6a5acd", + linen: "#faf0e6", + darkblue: "#00008b", + powderblue: "#b0e0e6", + seagreen: "#2e8b57", + darkkhaki: "#bdb76b", + snow: "#fffafa", + sienna: "#a0522d", + mediumblue: "#0000cd", + royalblue: "#4169e1", + lightcyan: "#e0ffff", + green: "#008000", + mediumpurple: "#9370db", + midnightblue: "#191970", + cornsilk: "#fff8dc", + paleturquoise: "#afeeee", + bisque: "#ffe4c4", + slategray: "#708090", + darkcyan: "#008b8b", + khaki: "#f0e68c", + wheat: "#f5deb3", + teal: "#008080", + darkorchid: "#9932cc", + deepskyblue: "#00bfff", + salmon: "#fa8072", + darkred: "#8b0000", + steelblue: "#4682b4", + palevioletred: "#db7093", + lightslategray: "#778899", + aliceblue: "#f0f8ff", + lightslategrey: "#778899", + lightgreen: "#90ee90", + orchid: "#da70d6", + gainsboro: "#dcdcdc", + mediumseagreen: "#3cb371", + lightgray: "#d3d3d3", + mediumturquoise: "#48d1cc", + lemonchiffon: "#fffacd", + cadetblue: "#5f9ea0", + lightyellow: "#ffffe0", + lavenderblush: "#fff0f5", + coral: "#ff7f50", + purple: "#800080", + aqua: "#00ffff", + whitesmoke: "#f5f5f5", + mediumslateblue: "#7b68ee", + darkorange: "#ff8c00", + mediumaquamarine: "#66cdaa", + darksalmon: "#e9967a", + beige: "#f5f5dc", + blueviolet: "#8a2be2", + azure: "#f0ffff", + lightsteelblue: "#b0c4de", + oldlace: "#fdf5e6", + rebeccapurple: "#663399" + }; + + chroma.colors = colors = w3cx11; + + lab2rgb = function() { + var a, args, b, g, l, r, x, y, z; + args = unpack(arguments); + l = args[0], a = args[1], b = args[2]; + y = (l + 16) / 116; + x = isNaN(a) ? y : y + a / 500; + z = isNaN(b) ? y : y - b / 200; + y = LAB_CONSTANTS.Yn * lab_xyz(y); + x = LAB_CONSTANTS.Xn * lab_xyz(x); + z = LAB_CONSTANTS.Zn * lab_xyz(z); + r = xyz_rgb(3.2404542 * x - 1.5371385 * y - 0.4985314 * z); + g = xyz_rgb(-0.9692660 * x + 1.8760108 * y + 0.0415560 * z); + b = xyz_rgb(0.0556434 * x - 0.2040259 * y + 1.0572252 * z); + r = limit(r, 0, 255); + g = limit(g, 0, 255); + b = limit(b, 0, 255); + return [r, g, b, args.length > 3 ? args[3] : 1]; + }; + + xyz_rgb = function(r) { + return round(255 * (r <= 0.00304 ? 12.92 * r : 1.055 * pow(r, 1 / 2.4) - 0.055)); + }; + + lab_xyz = function(t) { + if (t > LAB_CONSTANTS.t1) { + return t * t * t; + } else { + return LAB_CONSTANTS.t2 * (t - LAB_CONSTANTS.t0); + } + }; + + LAB_CONSTANTS = { + Kn: 18, + Xn: 0.950470, + Yn: 1, + Zn: 1.088830, + t0: 0.137931034, + t1: 0.206896552, + t2: 0.12841855, + t3: 0.008856452 + }; + + rgb2lab = function() { + var b, g, r, ref, ref1, x, y, z; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + ref1 = rgb2xyz(r, g, b), x = ref1[0], y = ref1[1], z = ref1[2]; + return [116 * y - 16, 500 * (x - y), 200 * (y - z)]; + }; + + rgb_xyz = function(r) { + if ((r /= 255) <= 0.04045) { + return r / 12.92; + } else { + return pow((r + 0.055) / 1.055, 2.4); + } + }; + + xyz_lab = function(t) { + if (t > LAB_CONSTANTS.t3) { + return pow(t, 1 / 3); + } else { + return t / LAB_CONSTANTS.t2 + LAB_CONSTANTS.t0; + } + }; + + rgb2xyz = function() { + var b, g, r, ref, x, y, z; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + r = rgb_xyz(r); + g = rgb_xyz(g); + b = rgb_xyz(b); + x = xyz_lab((0.4124564 * r + 0.3575761 * g + 0.1804375 * b) / LAB_CONSTANTS.Xn); + y = xyz_lab((0.2126729 * r + 0.7151522 * g + 0.0721750 * b) / LAB_CONSTANTS.Yn); + z = xyz_lab((0.0193339 * r + 0.1191920 * g + 0.9503041 * b) / LAB_CONSTANTS.Zn); + return [x, y, z]; + }; + + chroma.lab = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['lab']), function(){}); + }; + + _input.lab = lab2rgb; + + Color.prototype.lab = function() { + return rgb2lab(this._rgb); + }; + + bezier = function(colors) { + var I, I0, I1, c, lab0, lab1, lab2, lab3, ref, ref1, ref2; + colors = (function() { + var len, o, results; + results = []; + for (o = 0, len = colors.length; o < len; o++) { + c = colors[o]; + results.push(chroma(c)); + } + return results; + })(); + if (colors.length === 2) { + ref = (function() { + var len, o, results; + results = []; + for (o = 0, len = colors.length; o < len; o++) { + c = colors[o]; + results.push(c.lab()); + } + return results; + })(), lab0 = ref[0], lab1 = ref[1]; + I = function(t) { + var i, lab; + lab = (function() { + var o, results; + results = []; + for (i = o = 0; o <= 2; i = ++o) { + results.push(lab0[i] + t * (lab1[i] - lab0[i])); + } + return results; + })(); + return chroma.lab.apply(chroma, lab); + }; + } else if (colors.length === 3) { + ref1 = (function() { + var len, o, results; + results = []; + for (o = 0, len = colors.length; o < len; o++) { + c = colors[o]; + results.push(c.lab()); + } + return results; + })(), lab0 = ref1[0], lab1 = ref1[1], lab2 = ref1[2]; + I = function(t) { + var i, lab; + lab = (function() { + var o, results; + results = []; + for (i = o = 0; o <= 2; i = ++o) { + results.push((1 - t) * (1 - t) * lab0[i] + 2 * (1 - t) * t * lab1[i] + t * t * lab2[i]); + } + return results; + })(); + return chroma.lab.apply(chroma, lab); + }; + } else if (colors.length === 4) { + ref2 = (function() { + var len, o, results; + results = []; + for (o = 0, len = colors.length; o < len; o++) { + c = colors[o]; + results.push(c.lab()); + } + return results; + })(), lab0 = ref2[0], lab1 = ref2[1], lab2 = ref2[2], lab3 = ref2[3]; + I = function(t) { + var i, lab; + lab = (function() { + var o, results; + results = []; + for (i = o = 0; o <= 2; i = ++o) { + results.push((1 - t) * (1 - t) * (1 - t) * lab0[i] + 3 * (1 - t) * (1 - t) * t * lab1[i] + 3 * (1 - t) * t * t * lab2[i] + t * t * t * lab3[i]); + } + return results; + })(); + return chroma.lab.apply(chroma, lab); + }; + } else if (colors.length === 5) { + I0 = bezier(colors.slice(0, 3)); + I1 = bezier(colors.slice(2, 5)); + I = function(t) { + if (t < 0.5) { + return I0(t * 2); + } else { + return I1((t - 0.5) * 2); + } + }; + } + return I; + }; + + chroma.bezier = function(colors) { + var f; + f = bezier(colors); + f.scale = function() { + return chroma.scale(f); + }; + return f; + }; + + + /* + chroma.js + + Copyright (c) 2011-2013, Gregor Aisch + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + + * The name Gregor Aisch may not be used to endorse or promote products + derived from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL GREGOR AISCH OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, + INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY + OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + @source: https://github.com/gka/chroma.js + */ + + chroma.cubehelix = function(start, rotations, hue, gamma, lightness) { + var dh, dl, f; + if (start == null) { + start = 300; + } + if (rotations == null) { + rotations = -1.5; + } + if (hue == null) { + hue = 1; + } + if (gamma == null) { + gamma = 1; + } + if (lightness == null) { + lightness = [0, 1]; + } + dl = lightness[1] - lightness[0]; + dh = 0; + f = function(fract) { + var a, amp, b, cos_a, g, h, l, r, sin_a; + a = TWOPI * ((start + 120) / 360 + rotations * fract); + l = pow(lightness[0] + dl * fract, gamma); + h = dh !== 0 ? hue[0] + fract * dh : hue; + amp = h * l * (1 - l) / 2; + cos_a = cos(a); + sin_a = sin(a); + r = l + amp * (-0.14861 * cos_a + 1.78277 * sin_a); + g = l + amp * (-0.29227 * cos_a - 0.90649 * sin_a); + b = l + amp * (+1.97294 * cos_a); + return chroma(clip_rgb([r * 255, g * 255, b * 255])); + }; + f.start = function(s) { + if (s == null) { + return start; + } + start = s; + return f; + }; + f.rotations = function(r) { + if (r == null) { + return rotations; + } + rotations = r; + return f; + }; + f.gamma = function(g) { + if (g == null) { + return gamma; + } + gamma = g; + return f; + }; + f.hue = function(h) { + if (h == null) { + return hue; + } + hue = h; + if (type(hue) === 'array') { + dh = hue[1] - hue[0]; + if (dh === 0) { + hue = hue[1]; + } + } else { + dh = 0; + } + return f; + }; + f.lightness = function(h) { + if (h == null) { + return lightness; + } + lightness = h; + if (type(lightness) === 'array') { + dl = lightness[1] - lightness[0]; + if (dl === 0) { + lightness = lightness[1]; + } + } else { + dl = 0; + } + return f; + }; + f.scale = function() { + return chroma.scale(f); + }; + f.hue(hue); + return f; + }; + + chroma.random = function() { + var code, digits, i, o; + digits = '0123456789abcdef'; + code = '#'; + for (i = o = 0; o < 6; i = ++o) { + code += digits.charAt(floor(Math.random() * 16)); + } + return new Color(code); + }; + + _input.rgb = function() { + var k, ref, results, v; + ref = unpack(arguments); + results = []; + for (k in ref) { + v = ref[k]; + results.push(v); + } + return results; + }; + + chroma.rgb = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['rgb']), function(){}); + }; + + Color.prototype.rgb = function() { + return this._rgb.slice(0, 3); + }; + + Color.prototype.rgba = function() { + return this._rgb; + }; + + _guess_formats.push({ + p: 15, + test: function(n) { + var a; + a = unpack(arguments); + if (type(a) === 'array' && a.length === 3) { + return 'rgb'; + } + if (a.length === 4 && type(a[3]) === "number" && a[3] >= 0 && a[3] <= 1) { + return 'rgb'; + } + } + }); + + hex2rgb = function(hex) { + var a, b, g, r, rgb, u; + if (hex.match(/^#?([A-Fa-f0-9]{6}|[A-Fa-f0-9]{3})$/)) { + if (hex.length === 4 || hex.length === 7) { + hex = hex.substr(1); + } + if (hex.length === 3) { + hex = hex.split(""); + hex = hex[0] + hex[0] + hex[1] + hex[1] + hex[2] + hex[2]; + } + u = parseInt(hex, 16); + r = u >> 16; + g = u >> 8 & 0xFF; + b = u & 0xFF; + return [r, g, b, 1]; + } + if (hex.match(/^#?([A-Fa-f0-9]{8})$/)) { + if (hex.length === 9) { + hex = hex.substr(1); + } + u = parseInt(hex, 16); + r = u >> 24 & 0xFF; + g = u >> 16 & 0xFF; + b = u >> 8 & 0xFF; + a = round((u & 0xFF) / 0xFF * 100) / 100; + return [r, g, b, a]; + } + if ((_input.css != null) && (rgb = _input.css(hex))) { + return rgb; + } + throw "unknown color: " + hex; + }; + + rgb2hex = function(channels, mode) { + var a, b, g, hxa, r, str, u; + if (mode == null) { + mode = 'rgb'; + } + r = channels[0], g = channels[1], b = channels[2], a = channels[3]; + u = r << 16 | g << 8 | b; + str = "000000" + u.toString(16); + str = str.substr(str.length - 6); + hxa = '0' + round(a * 255).toString(16); + hxa = hxa.substr(hxa.length - 2); + return "#" + (function() { + switch (mode.toLowerCase()) { + case 'rgba': + return str + hxa; + case 'argb': + return hxa + str; + default: + return str; + } + })(); + }; + + _input.hex = function(h) { + return hex2rgb(h); + }; + + chroma.hex = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['hex']), function(){}); + }; + + Color.prototype.hex = function(mode) { + if (mode == null) { + mode = 'rgb'; + } + return rgb2hex(this._rgb, mode); + }; + + _guess_formats.push({ + p: 10, + test: function(n) { + if (arguments.length === 1 && type(n) === "string") { + return 'hex'; + } + } + }); + + hsl2rgb = function() { + var args, b, c, g, h, i, l, o, r, ref, s, t1, t2, t3; + args = unpack(arguments); + h = args[0], s = args[1], l = args[2]; + if (s === 0) { + r = g = b = l * 255; + } else { + t3 = [0, 0, 0]; + c = [0, 0, 0]; + t2 = l < 0.5 ? l * (1 + s) : l + s - l * s; + t1 = 2 * l - t2; + h /= 360; + t3[0] = h + 1 / 3; + t3[1] = h; + t3[2] = h - 1 / 3; + for (i = o = 0; o <= 2; i = ++o) { + if (t3[i] < 0) { + t3[i] += 1; + } + if (t3[i] > 1) { + t3[i] -= 1; + } + if (6 * t3[i] < 1) { + c[i] = t1 + (t2 - t1) * 6 * t3[i]; + } else if (2 * t3[i] < 1) { + c[i] = t2; + } else if (3 * t3[i] < 2) { + c[i] = t1 + (t2 - t1) * ((2 / 3) - t3[i]) * 6; + } else { + c[i] = t1; + } + } + ref = [round(c[0] * 255), round(c[1] * 255), round(c[2] * 255)], r = ref[0], g = ref[1], b = ref[2]; + } + if (args.length > 3) { + return [r, g, b, args[3]]; + } else { + return [r, g, b]; + } + }; + + rgb2hsl = function(r, g, b) { + var h, l, min, ref, s; + if (r !== void 0 && r.length >= 3) { + ref = r, r = ref[0], g = ref[1], b = ref[2]; + } + r /= 255; + g /= 255; + b /= 255; + min = Math.min(r, g, b); + max = Math.max(r, g, b); + l = (max + min) / 2; + if (max === min) { + s = 0; + h = Number.NaN; + } else { + s = l < 0.5 ? (max - min) / (max + min) : (max - min) / (2 - max - min); + } + if (r === max) { + h = (g - b) / (max - min); + } else if (g === max) { + h = 2 + (b - r) / (max - min); + } else if (b === max) { + h = 4 + (r - g) / (max - min); + } + h *= 60; + if (h < 0) { + h += 360; + } + return [h, s, l]; + }; + + chroma.hsl = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['hsl']), function(){}); + }; + + _input.hsl = hsl2rgb; + + Color.prototype.hsl = function() { + return rgb2hsl(this._rgb); + }; + + hsv2rgb = function() { + var args, b, f, g, h, i, p, q, r, ref, ref1, ref2, ref3, ref4, ref5, s, t, v; + args = unpack(arguments); + h = args[0], s = args[1], v = args[2]; + v *= 255; + if (s === 0) { + r = g = b = v; + } else { + if (h === 360) { + h = 0; + } + if (h > 360) { + h -= 360; + } + if (h < 0) { + h += 360; + } + h /= 60; + i = floor(h); + f = h - i; + p = v * (1 - s); + q = v * (1 - s * f); + t = v * (1 - s * (1 - f)); + switch (i) { + case 0: + ref = [v, t, p], r = ref[0], g = ref[1], b = ref[2]; + break; + case 1: + ref1 = [q, v, p], r = ref1[0], g = ref1[1], b = ref1[2]; + break; + case 2: + ref2 = [p, v, t], r = ref2[0], g = ref2[1], b = ref2[2]; + break; + case 3: + ref3 = [p, q, v], r = ref3[0], g = ref3[1], b = ref3[2]; + break; + case 4: + ref4 = [t, p, v], r = ref4[0], g = ref4[1], b = ref4[2]; + break; + case 5: + ref5 = [v, p, q], r = ref5[0], g = ref5[1], b = ref5[2]; + } + } + r = round(r); + g = round(g); + b = round(b); + return [r, g, b, args.length > 3 ? args[3] : 1]; + }; + + rgb2hsv = function() { + var b, delta, g, h, min, r, ref, s, v; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + min = Math.min(r, g, b); + max = Math.max(r, g, b); + delta = max - min; + v = max / 255.0; + if (max === 0) { + h = Number.NaN; + s = 0; + } else { + s = delta / max; + if (r === max) { + h = (g - b) / delta; + } + if (g === max) { + h = 2 + (b - r) / delta; + } + if (b === max) { + h = 4 + (r - g) / delta; + } + h *= 60; + if (h < 0) { + h += 360; + } + } + return [h, s, v]; + }; + + chroma.hsv = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['hsv']), function(){}); + }; + + _input.hsv = hsv2rgb; + + Color.prototype.hsv = function() { + return rgb2hsv(this._rgb); + }; + + num2rgb = function(num) { + var b, g, r; + if (type(num) === "number" && num >= 0 && num <= 0xFFFFFF) { + r = num >> 16; + g = (num >> 8) & 0xFF; + b = num & 0xFF; + return [r, g, b, 1]; + } + console.warn("unknown num color: " + num); + return [0, 0, 0, 1]; + }; + + rgb2num = function() { + var b, g, r, ref; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + return (r << 16) + (g << 8) + b; + }; + + chroma.num = function(num) { + return new Color(num, 'num'); + }; + + Color.prototype.num = function(mode) { + if (mode == null) { + mode = 'rgb'; + } + return rgb2num(this._rgb, mode); + }; + + _input.num = num2rgb; + + _guess_formats.push({ + p: 10, + test: function(n) { + if (arguments.length === 1 && type(n) === "number" && n >= 0 && n <= 0xFFFFFF) { + return 'num'; + } + } + }); + + css2rgb = function(css) { + var aa, ab, hsl, i, m, o, rgb, w; + css = css.toLowerCase(); + if ((chroma.colors != null) && chroma.colors[css]) { + return hex2rgb(chroma.colors[css]); + } + if (m = css.match(/rgb\(\s*(\-?\d+),\s*(\-?\d+)\s*,\s*(\-?\d+)\s*\)/)) { + rgb = m.slice(1, 4); + for (i = o = 0; o <= 2; i = ++o) { + rgb[i] = +rgb[i]; + } + rgb[3] = 1; + } else if (m = css.match(/rgba\(\s*(\-?\d+),\s*(\-?\d+)\s*,\s*(\-?\d+)\s*,\s*([01]|[01]?\.\d+)\)/)) { + rgb = m.slice(1, 5); + for (i = w = 0; w <= 3; i = ++w) { + rgb[i] = +rgb[i]; + } + } else if (m = css.match(/rgb\(\s*(\-?\d+(?:\.\d+)?)%,\s*(\-?\d+(?:\.\d+)?)%\s*,\s*(\-?\d+(?:\.\d+)?)%\s*\)/)) { + rgb = m.slice(1, 4); + for (i = aa = 0; aa <= 2; i = ++aa) { + rgb[i] = round(rgb[i] * 2.55); + } + rgb[3] = 1; + } else if (m = css.match(/rgba\(\s*(\-?\d+(?:\.\d+)?)%,\s*(\-?\d+(?:\.\d+)?)%\s*,\s*(\-?\d+(?:\.\d+)?)%\s*,\s*([01]|[01]?\.\d+)\)/)) { + rgb = m.slice(1, 5); + for (i = ab = 0; ab <= 2; i = ++ab) { + rgb[i] = round(rgb[i] * 2.55); + } + rgb[3] = +rgb[3]; + } else if (m = css.match(/hsl\(\s*(\-?\d+(?:\.\d+)?),\s*(\-?\d+(?:\.\d+)?)%\s*,\s*(\-?\d+(?:\.\d+)?)%\s*\)/)) { + hsl = m.slice(1, 4); + hsl[1] *= 0.01; + hsl[2] *= 0.01; + rgb = hsl2rgb(hsl); + rgb[3] = 1; + } else if (m = css.match(/hsla\(\s*(\-?\d+(?:\.\d+)?),\s*(\-?\d+(?:\.\d+)?)%\s*,\s*(\-?\d+(?:\.\d+)?)%\s*,\s*([01]|[01]?\.\d+)\)/)) { + hsl = m.slice(1, 4); + hsl[1] *= 0.01; + hsl[2] *= 0.01; + rgb = hsl2rgb(hsl); + rgb[3] = +m[4]; + } + return rgb; + }; + + rgb2css = function(rgba) { + var mode; + mode = rgba[3] < 1 ? 'rgba' : 'rgb'; + if (mode === 'rgb') { + return mode + '(' + rgba.slice(0, 3).map(round).join(',') + ')'; + } else if (mode === 'rgba') { + return mode + '(' + rgba.slice(0, 3).map(round).join(',') + ',' + rgba[3] + ')'; + } else { + + } + }; + + rnd = function(a) { + return round(a * 100) / 100; + }; + + hsl2css = function(hsl, alpha) { + var mode; + mode = alpha < 1 ? 'hsla' : 'hsl'; + hsl[0] = rnd(hsl[0] || 0); + hsl[1] = rnd(hsl[1] * 100) + '%'; + hsl[2] = rnd(hsl[2] * 100) + '%'; + if (mode === 'hsla') { + hsl[3] = alpha; + } + return mode + '(' + hsl.join(',') + ')'; + }; + + _input.css = function(h) { + return css2rgb(h); + }; + + chroma.css = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['css']), function(){}); + }; + + Color.prototype.css = function(mode) { + if (mode == null) { + mode = 'rgb'; + } + if (mode.slice(0, 3) === 'rgb') { + return rgb2css(this._rgb); + } else if (mode.slice(0, 3) === 'hsl') { + return hsl2css(this.hsl(), this.alpha()); + } + }; + + _input.named = function(name) { + return hex2rgb(w3cx11[name]); + }; + + _guess_formats.push({ + p: 20, + test: function(n) { + if (arguments.length === 1 && (w3cx11[n] != null)) { + return 'named'; + } + } + }); + + Color.prototype.name = function(n) { + var h, k; + if (arguments.length) { + if (w3cx11[n]) { + this._rgb = hex2rgb(w3cx11[n]); + } + this._rgb[3] = 1; + this; + } + h = this.hex(); + for (k in w3cx11) { + if (h === w3cx11[k]) { + return k; + } + } + return h; + }; + + lch2lab = function() { + + /* + Convert from a qualitative parameter h and a quantitative parameter l to a 24-bit pixel. + These formulas were invented by David Dalrymple to obtain maximum contrast without going + out of gamut if the parameters are in the range 0-1. + + A saturation multiplier was added by Gregor Aisch + */ + var c, h, l, ref; + ref = unpack(arguments), l = ref[0], c = ref[1], h = ref[2]; + h = h * DEG2RAD; + return [l, cos(h) * c, sin(h) * c]; + }; + + lch2rgb = function() { + var L, a, args, b, c, g, h, l, r, ref, ref1; + args = unpack(arguments); + l = args[0], c = args[1], h = args[2]; + ref = lch2lab(l, c, h), L = ref[0], a = ref[1], b = ref[2]; + ref1 = lab2rgb(L, a, b), r = ref1[0], g = ref1[1], b = ref1[2]; + return [limit(r, 0, 255), limit(g, 0, 255), limit(b, 0, 255), args.length > 3 ? args[3] : 1]; + }; + + lab2lch = function() { + var a, b, c, h, l, ref; + ref = unpack(arguments), l = ref[0], a = ref[1], b = ref[2]; + c = sqrt(a * a + b * b); + h = (atan2(b, a) * RAD2DEG + 360) % 360; + if (round(c * 10000) === 0) { + h = Number.NaN; + } + return [l, c, h]; + }; + + rgb2lch = function() { + var a, b, g, l, r, ref, ref1; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + ref1 = rgb2lab(r, g, b), l = ref1[0], a = ref1[1], b = ref1[2]; + return lab2lch(l, a, b); + }; + + chroma.lch = function() { + var args; + args = unpack(arguments); + return new Color(args, 'lch'); + }; + + chroma.hcl = function() { + var args; + args = unpack(arguments); + return new Color(args, 'hcl'); + }; + + _input.lch = lch2rgb; + + _input.hcl = function() { + var c, h, l, ref; + ref = unpack(arguments), h = ref[0], c = ref[1], l = ref[2]; + return lch2rgb([l, c, h]); + }; + + Color.prototype.lch = function() { + return rgb2lch(this._rgb); + }; + + Color.prototype.hcl = function() { + return rgb2lch(this._rgb).reverse(); + }; + + rgb2cmyk = function(mode) { + var b, c, f, g, k, m, r, ref, y; + if (mode == null) { + mode = 'rgb'; + } + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + r = r / 255; + g = g / 255; + b = b / 255; + k = 1 - Math.max(r, Math.max(g, b)); + f = k < 1 ? 1 / (1 - k) : 0; + c = (1 - r - k) * f; + m = (1 - g - k) * f; + y = (1 - b - k) * f; + return [c, m, y, k]; + }; + + cmyk2rgb = function() { + var alpha, args, b, c, g, k, m, r, y; + args = unpack(arguments); + c = args[0], m = args[1], y = args[2], k = args[3]; + alpha = args.length > 4 ? args[4] : 1; + if (k === 1) { + return [0, 0, 0, alpha]; + } + r = c >= 1 ? 0 : round(255 * (1 - c) * (1 - k)); + g = m >= 1 ? 0 : round(255 * (1 - m) * (1 - k)); + b = y >= 1 ? 0 : round(255 * (1 - y) * (1 - k)); + return [r, g, b, alpha]; + }; + + _input.cmyk = function() { + return cmyk2rgb(unpack(arguments)); + }; + + chroma.cmyk = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['cmyk']), function(){}); + }; + + Color.prototype.cmyk = function() { + return rgb2cmyk(this._rgb); + }; + + _input.gl = function() { + var i, k, o, rgb, v; + rgb = (function() { + var ref, results; + ref = unpack(arguments); + results = []; + for (k in ref) { + v = ref[k]; + results.push(v); + } + return results; + }).apply(this, arguments); + for (i = o = 0; o <= 2; i = ++o) { + rgb[i] *= 255; + } + return rgb; + }; + + chroma.gl = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['gl']), function(){}); + }; + + Color.prototype.gl = function() { + var rgb; + rgb = this._rgb; + return [rgb[0] / 255, rgb[1] / 255, rgb[2] / 255, rgb[3]]; + }; + + rgb2luminance = function(r, g, b) { + var ref; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + r = luminance_x(r); + g = luminance_x(g); + b = luminance_x(b); + return 0.2126 * r + 0.7152 * g + 0.0722 * b; + }; + + luminance_x = function(x) { + x /= 255; + if (x <= 0.03928) { + return x / 12.92; + } else { + return pow((x + 0.055) / 1.055, 2.4); + } + }; + + _interpolators = []; + + interpolate = function(col1, col2, f, m) { + var interpol, len, o, res; + if (f == null) { + f = 0.5; + } + if (m == null) { + m = 'rgb'; + } + + /* + interpolates between colors + f = 0 --> me + f = 1 --> col + */ + if (type(col1) !== 'object') { + col1 = chroma(col1); + } + if (type(col2) !== 'object') { + col2 = chroma(col2); + } + for (o = 0, len = _interpolators.length; o < len; o++) { + interpol = _interpolators[o]; + if (m === interpol[0]) { + res = interpol[1](col1, col2, f, m); + break; + } + } + if (res == null) { + throw "color mode " + m + " is not supported"; + } + res.alpha(col1.alpha() + f * (col2.alpha() - col1.alpha())); + return res; + }; + + chroma.interpolate = interpolate; + + Color.prototype.interpolate = function(col2, f, m) { + return interpolate(this, col2, f, m); + }; + + chroma.mix = interpolate; + + Color.prototype.mix = Color.prototype.interpolate; + + interpolate_rgb = function(col1, col2, f, m) { + var xyz0, xyz1; + xyz0 = col1._rgb; + xyz1 = col2._rgb; + return new Color(xyz0[0] + f * (xyz1[0] - xyz0[0]), xyz0[1] + f * (xyz1[1] - xyz0[1]), xyz0[2] + f * (xyz1[2] - xyz0[2]), m); + }; + + _interpolators.push(['rgb', interpolate_rgb]); + + Color.prototype.luminance = function(lum, mode) { + var cur_lum, eps, max_iter, test; + if (mode == null) { + mode = 'rgb'; + } + if (!arguments.length) { + return rgb2luminance(this._rgb); + } + if (lum === 0) { + this._rgb = [0, 0, 0, this._rgb[3]]; + } else if (lum === 1) { + this._rgb = [255, 255, 255, this._rgb[3]]; + } else { + eps = 1e-7; + max_iter = 20; + test = function(l, h) { + var lm, m; + m = l.interpolate(h, 0.5, mode); + lm = m.luminance(); + if (Math.abs(lum - lm) < eps || !max_iter--) { + return m; + } + if (lm > lum) { + return test(l, m); + } + return test(m, h); + }; + cur_lum = rgb2luminance(this._rgb); + this._rgb = (cur_lum > lum ? test(chroma('black'), this) : test(this, chroma('white'))).rgba(); + } + return this; + }; + + temperature2rgb = function(kelvin) { + var b, g, r, temp; + temp = kelvin / 100; + if (temp < 66) { + r = 255; + g = -155.25485562709179 - 0.44596950469579133 * (g = temp - 2) + 104.49216199393888 * log(g); + b = temp < 20 ? 0 : -254.76935184120902 + 0.8274096064007395 * (b = temp - 10) + 115.67994401066147 * log(b); + } else { + r = 351.97690566805693 + 0.114206453784165 * (r = temp - 55) - 40.25366309332127 * log(r); + g = 325.4494125711974 + 0.07943456536662342 * (g = temp - 50) - 28.0852963507957 * log(g); + b = 255; + } + return clip_rgb([r, g, b]); + }; + + rgb2temperature = function() { + var b, eps, g, maxTemp, minTemp, r, ref, rgb, temp; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + minTemp = 1000; + maxTemp = 40000; + eps = 0.4; + while (maxTemp - minTemp > eps) { + temp = (maxTemp + minTemp) * 0.5; + rgb = temperature2rgb(temp); + if ((rgb[2] / rgb[0]) >= (b / r)) { + maxTemp = temp; + } else { + minTemp = temp; + } + } + return round(temp); + }; + + chroma.temperature = chroma.kelvin = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['temperature']), function(){}); + }; + + _input.temperature = _input.kelvin = _input.K = temperature2rgb; + + Color.prototype.temperature = function() { + return rgb2temperature(this._rgb); + }; + + Color.prototype.kelvin = Color.prototype.temperature; + + chroma.contrast = function(a, b) { + var l1, l2, ref, ref1; + if ((ref = type(a)) === 'string' || ref === 'number') { + a = new Color(a); + } + if ((ref1 = type(b)) === 'string' || ref1 === 'number') { + b = new Color(b); + } + l1 = a.luminance(); + l2 = b.luminance(); + if (l1 > l2) { + return (l1 + 0.05) / (l2 + 0.05); + } else { + return (l2 + 0.05) / (l1 + 0.05); + } + }; + + Color.prototype.get = function(modechan) { + var channel, i, me, mode, ref, src; + me = this; + ref = modechan.split('.'), mode = ref[0], channel = ref[1]; + src = me[mode](); + if (channel) { + i = mode.indexOf(channel); + if (i > -1) { + return src[i]; + } else { + return console.warn('unknown channel ' + channel + ' in mode ' + mode); + } + } else { + return src; + } + }; + + Color.prototype.set = function(modechan, value) { + var channel, i, me, mode, ref, src; + me = this; + ref = modechan.split('.'), mode = ref[0], channel = ref[1]; + if (channel) { + src = me[mode](); + i = mode.indexOf(channel); + if (i > -1) { + if (type(value) === 'string') { + switch (value.charAt(0)) { + case '+': + src[i] += +value; + break; + case '-': + src[i] += +value; + break; + case '*': + src[i] *= +(value.substr(1)); + break; + case '/': + src[i] /= +(value.substr(1)); + break; + default: + src[i] = +value; + } + } else { + src[i] = value; + } + } else { + console.warn('unknown channel ' + channel + ' in mode ' + mode); + } + } else { + src = value; + } + me._rgb = chroma(src, mode).alpha(me.alpha())._rgb; + return me; + }; + + Color.prototype.darken = function(amount) { + var lab, me; + if (amount == null) { + amount = 1; + } + me = this; + lab = me.lab(); + lab[0] -= LAB_CONSTANTS.Kn * amount; + return chroma.lab(lab).alpha(me.alpha()); + }; + + Color.prototype.brighten = function(amount) { + if (amount == null) { + amount = 1; + } + return this.darken(-amount); + }; + + Color.prototype.darker = Color.prototype.darken; + + Color.prototype.brighter = Color.prototype.brighten; + + Color.prototype.saturate = function(amount) { + var lch, me; + if (amount == null) { + amount = 1; + } + me = this; + lch = me.lch(); + lch[1] += amount * LAB_CONSTANTS.Kn; + if (lch[1] < 0) { + lch[1] = 0; + } + return chroma.lch(lch).alpha(me.alpha()); + }; + + Color.prototype.desaturate = function(amount) { + if (amount == null) { + amount = 1; + } + return this.saturate(-amount); + }; + + Color.prototype.premultiply = function() { + var a, rgb; + rgb = this.rgb(); + a = this.alpha(); + return chroma(rgb[0] * a, rgb[1] * a, rgb[2] * a, a); + }; + + blend = function(bottom, top, mode) { + if (!blend[mode]) { + throw 'unknown blend mode ' + mode; + } + return blend[mode](bottom, top); + }; + + blend_f = function(f) { + return function(bottom, top) { + var c0, c1; + c0 = chroma(top).rgb(); + c1 = chroma(bottom).rgb(); + return chroma(f(c0, c1), 'rgb'); + }; + }; + + each = function(f) { + return function(c0, c1) { + var i, o, out; + out = []; + for (i = o = 0; o <= 3; i = ++o) { + out[i] = f(c0[i], c1[i]); + } + return out; + }; + }; + + normal = function(a, b) { + return a; + }; + + multiply = function(a, b) { + return a * b / 255; + }; + + darken = function(a, b) { + if (a > b) { + return b; + } else { + return a; + } + }; + + lighten = function(a, b) { + if (a > b) { + return a; + } else { + return b; + } + }; + + screen = function(a, b) { + return 255 * (1 - (1 - a / 255) * (1 - b / 255)); + }; + + overlay = function(a, b) { + if (b < 128) { + return 2 * a * b / 255; + } else { + return 255 * (1 - 2 * (1 - a / 255) * (1 - b / 255)); + } + }; + + burn = function(a, b) { + return 255 * (1 - (1 - b / 255) / (a / 255)); + }; + + dodge = function(a, b) { + if (a === 255) { + return 255; + } + a = 255 * (b / 255) / (1 - a / 255); + if (a > 255) { + return 255; + } else { + return a; + } + }; + + blend.normal = blend_f(each(normal)); + + blend.multiply = blend_f(each(multiply)); + + blend.screen = blend_f(each(screen)); + + blend.overlay = blend_f(each(overlay)); + + blend.darken = blend_f(each(darken)); + + blend.lighten = blend_f(each(lighten)); + + blend.dodge = blend_f(each(dodge)); + + blend.burn = blend_f(each(burn)); + + chroma.blend = blend; + + chroma.analyze = function(data) { + var len, o, r, val; + r = { + min: Number.MAX_VALUE, + max: Number.MAX_VALUE * -1, + sum: 0, + values: [], + count: 0 + }; + for (o = 0, len = data.length; o < len; o++) { + val = data[o]; + if ((val != null) && !isNaN(val)) { + r.values.push(val); + r.sum += val; + if (val < r.min) { + r.min = val; + } + if (val > r.max) { + r.max = val; + } + r.count += 1; + } + } + r.domain = [r.min, r.max]; + r.limits = function(mode, num) { + return chroma.limits(r, mode, num); + }; + return r; + }; + + chroma.scale = function(colors, positions) { + var _classes, _colorCache, _colors, _correctLightness, _domain, _fixed, _max, _min, _mode, _nacol, _out, _padding, _pos, _spread, classifyValue, f, getClass, getColor, resetCache, setColors, tmap; + _mode = 'rgb'; + _nacol = chroma('#ccc'); + _spread = 0; + _fixed = false; + _domain = [0, 1]; + _pos = []; + _padding = [0, 0]; + _classes = false; + _colors = []; + _out = false; + _min = 0; + _max = 1; + _correctLightness = false; + _colorCache = {}; + setColors = function(colors) { + var c, col, o, ref, ref1, ref2, w; + if (colors == null) { + colors = ['#fff', '#000']; + } + if ((colors != null) && type(colors) === 'string' && (((ref = chroma.brewer) != null ? ref[colors] : void 0) != null)) { + colors = chroma.brewer[colors]; + } + if (type(colors) === 'array') { + colors = colors.slice(0); + for (c = o = 0, ref1 = colors.length - 1; 0 <= ref1 ? o <= ref1 : o >= ref1; c = 0 <= ref1 ? ++o : --o) { + col = colors[c]; + if (type(col) === "string") { + colors[c] = chroma(col); + } + } + _pos.length = 0; + for (c = w = 0, ref2 = colors.length - 1; 0 <= ref2 ? w <= ref2 : w >= ref2; c = 0 <= ref2 ? ++w : --w) { + _pos.push(c / (colors.length - 1)); + } + } + resetCache(); + return _colors = colors; + }; + getClass = function(value) { + var i, n; + if (_classes != null) { + n = _classes.length - 1; + i = 0; + while (i < n && value >= _classes[i]) { + i++; + } + return i - 1; + } + return 0; + }; + tmap = function(t) { + return t; + }; + classifyValue = function(value) { + var i, maxc, minc, n, val; + val = value; + if (_classes.length > 2) { + n = _classes.length - 1; + i = getClass(value); + minc = _classes[0] + (_classes[1] - _classes[0]) * (0 + _spread * 0.5); + maxc = _classes[n - 1] + (_classes[n] - _classes[n - 1]) * (1 - _spread * 0.5); + val = _min + ((_classes[i] + (_classes[i + 1] - _classes[i]) * 0.5 - minc) / (maxc - minc)) * (_max - _min); + } + return val; + }; + getColor = function(val, bypassMap) { + var c, col, i, k, o, p, ref, t; + if (bypassMap == null) { + bypassMap = false; + } + if (isNaN(val)) { + return _nacol; + } + if (!bypassMap) { + if (_classes && _classes.length > 2) { + c = getClass(val); + t = c / (_classes.length - 2); + t = _padding[0] + (t * (1 - _padding[0] - _padding[1])); + } else if (_max !== _min) { + t = (val - _min) / (_max - _min); + t = _padding[0] + (t * (1 - _padding[0] - _padding[1])); + t = Math.min(1, Math.max(0, t)); + } else { + t = 1; + } + } else { + t = val; + } + if (!bypassMap) { + t = tmap(t); + } + k = Math.floor(t * 10000); + if (_colorCache[k]) { + col = _colorCache[k]; + } else { + if (type(_colors) === 'array') { + for (i = o = 0, ref = _pos.length - 1; 0 <= ref ? o <= ref : o >= ref; i = 0 <= ref ? ++o : --o) { + p = _pos[i]; + if (t <= p) { + col = _colors[i]; + break; + } + if (t >= p && i === _pos.length - 1) { + col = _colors[i]; + break; + } + if (t > p && t < _pos[i + 1]) { + t = (t - p) / (_pos[i + 1] - p); + col = chroma.interpolate(_colors[i], _colors[i + 1], t, _mode); + break; + } + } + } else if (type(_colors) === 'function') { + col = _colors(t); + } + _colorCache[k] = col; + } + return col; + }; + resetCache = function() { + return _colorCache = {}; + }; + setColors(colors); + f = function(v) { + var c; + c = chroma(getColor(v)); + if (_out && c[_out]) { + return c[_out](); + } else { + return c; + } + }; + f.classes = function(classes) { + var d; + if (classes != null) { + if (type(classes) === 'array') { + _classes = classes; + _domain = [classes[0], classes[classes.length - 1]]; + } else { + d = chroma.analyze(_domain); + if (classes === 0) { + _classes = [d.min, d.max]; + } else { + _classes = chroma.limits(d, 'e', classes); + } + } + return f; + } + return _classes; + }; + f.domain = function(domain) { + var c, d, k, len, o, ref, w; + if (!arguments.length) { + return _domain; + } + _min = domain[0]; + _max = domain[domain.length - 1]; + _pos = []; + k = _colors.length; + if (domain.length === k && _min !== _max) { + for (o = 0, len = domain.length; o < len; o++) { + d = domain[o]; + _pos.push((d - _min) / (_max - _min)); + } + } else { + for (c = w = 0, ref = k - 1; 0 <= ref ? w <= ref : w >= ref; c = 0 <= ref ? ++w : --w) { + _pos.push(c / (k - 1)); + } + } + _domain = [_min, _max]; + return f; + }; + f.mode = function(_m) { + if (!arguments.length) { + return _mode; + } + _mode = _m; + resetCache(); + return f; + }; + f.range = function(colors, _pos) { + setColors(colors, _pos); + return f; + }; + f.out = function(_o) { + _out = _o; + return f; + }; + f.spread = function(val) { + if (!arguments.length) { + return _spread; + } + _spread = val; + return f; + }; + f.correctLightness = function(v) { + if (v == null) { + v = true; + } + _correctLightness = v; + resetCache(); + if (_correctLightness) { + tmap = function(t) { + var L0, L1, L_actual, L_diff, L_ideal, max_iter, pol, t0, t1; + L0 = getColor(0, true).lab()[0]; + L1 = getColor(1, true).lab()[0]; + pol = L0 > L1; + L_actual = getColor(t, true).lab()[0]; + L_ideal = L0 + (L1 - L0) * t; + L_diff = L_actual - L_ideal; + t0 = 0; + t1 = 1; + max_iter = 20; + while (Math.abs(L_diff) > 1e-2 && max_iter-- > 0) { + (function() { + if (pol) { + L_diff *= -1; + } + if (L_diff < 0) { + t0 = t; + t += (t1 - t) * 0.5; + } else { + t1 = t; + t += (t0 - t) * 0.5; + } + L_actual = getColor(t, true).lab()[0]; + return L_diff = L_actual - L_ideal; + })(); + } + return t; + }; + } else { + tmap = function(t) { + return t; + }; + } + return f; + }; + f.padding = function(p) { + if (p != null) { + if (type(p) === 'number') { + p = [p, p]; + } + _padding = p; + return f; + } else { + return _padding; + } + }; + f.colors = function() { + var dd, dm, i, numColors, o, out, ref, results, samples, w; + numColors = 0; + out = 'hex'; + if (arguments.length === 1) { + if (type(arguments[0]) === 'string') { + out = arguments[0]; + } else { + numColors = arguments[0]; + } + } + if (arguments.length === 2) { + numColors = arguments[0], out = arguments[1]; + } + if (numColors) { + dm = _domain[0]; + dd = _domain[1] - dm; + return (function() { + results = []; + for (var o = 0; 0 <= numColors ? o < numColors : o > numColors; 0 <= numColors ? o++ : o--){ results.push(o); } + return results; + }).apply(this).map(function(i) { + return f(dm + i / (numColors - 1) * dd)[out](); + }); + } + colors = []; + samples = []; + if (_classes && _classes.length > 2) { + for (i = w = 1, ref = _classes.length; 1 <= ref ? w < ref : w > ref; i = 1 <= ref ? ++w : --w) { + samples.push((_classes[i - 1] + _classes[i]) * 0.5); + } + } else { + samples = _domain; + } + return samples.map(function(v) { + return f(v)[out](); + }); + }; + return f; + }; + + if (chroma.scales == null) { + chroma.scales = {}; + } + + chroma.scales.cool = function() { + return chroma.scale([chroma.hsl(180, 1, .9), chroma.hsl(250, .7, .4)]); + }; + + chroma.scales.hot = function() { + return chroma.scale(['#000', '#f00', '#ff0', '#fff'], [0, .25, .75, 1]).mode('rgb'); + }; + + chroma.analyze = function(data, key, filter) { + var add, k, len, o, r, val, visit; + r = { + min: Number.MAX_VALUE, + max: Number.MAX_VALUE * -1, + sum: 0, + values: [], + count: 0 + }; + if (filter == null) { + filter = function() { + return true; + }; + } + add = function(val) { + if ((val != null) && !isNaN(val)) { + r.values.push(val); + r.sum += val; + if (val < r.min) { + r.min = val; + } + if (val > r.max) { + r.max = val; + } + r.count += 1; + } + }; + visit = function(val, k) { + if (filter(val, k)) { + if ((key != null) && type(key) === 'function') { + return add(key(val)); + } else if ((key != null) && type(key) === 'string' || type(key) === 'number') { + return add(val[key]); + } else { + return add(val); + } + } + }; + if (type(data) === 'array') { + for (o = 0, len = data.length; o < len; o++) { + val = data[o]; + visit(val); + } + } else { + for (k in data) { + val = data[k]; + visit(val, k); + } + } + r.domain = [r.min, r.max]; + r.limits = function(mode, num) { + return chroma.limits(r, mode, num); + }; + return r; + }; + + chroma.limits = function(data, mode, num) { + var aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, assignments, best, centroids, cluster, clusterSizes, dist, i, j, kClusters, limits, max_log, min, min_log, mindist, n, nb_iters, newCentroids, o, p, pb, pr, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, repeat, sum, tmpKMeansBreaks, value, values, w; + if (mode == null) { + mode = 'equal'; + } + if (num == null) { + num = 7; + } + if (type(data) === 'array') { + data = chroma.analyze(data); + } + min = data.min; + max = data.max; + sum = data.sum; + values = data.values.sort(function(a, b) { + return a - b; + }); + limits = []; + if (mode.substr(0, 1) === 'c') { + limits.push(min); + limits.push(max); + } + if (mode.substr(0, 1) === 'e') { + limits.push(min); + for (i = o = 1, ref = num - 1; 1 <= ref ? o <= ref : o >= ref; i = 1 <= ref ? ++o : --o) { + limits.push(min + (i / num) * (max - min)); + } + limits.push(max); + } else if (mode.substr(0, 1) === 'l') { + if (min <= 0) { + throw 'Logarithmic scales are only possible for values > 0'; + } + min_log = Math.LOG10E * log(min); + max_log = Math.LOG10E * log(max); + limits.push(min); + for (i = w = 1, ref1 = num - 1; 1 <= ref1 ? w <= ref1 : w >= ref1; i = 1 <= ref1 ? ++w : --w) { + limits.push(pow(10, min_log + (i / num) * (max_log - min_log))); + } + limits.push(max); + } else if (mode.substr(0, 1) === 'q') { + limits.push(min); + for (i = aa = 1, ref2 = num - 1; 1 <= ref2 ? aa <= ref2 : aa >= ref2; i = 1 <= ref2 ? ++aa : --aa) { + p = values.length * i / num; + pb = floor(p); + if (pb === p) { + limits.push(values[pb]); + } else { + pr = p - pb; + limits.push(values[pb] * pr + values[pb + 1] * (1 - pr)); + } + } + limits.push(max); + } else if (mode.substr(0, 1) === 'k') { + + /* + implementation based on + http://code.google.com/p/figue/source/browse/trunk/figue.js#336 + simplified for 1-d input values + */ + n = values.length; + assignments = new Array(n); + clusterSizes = new Array(num); + repeat = true; + nb_iters = 0; + centroids = null; + centroids = []; + centroids.push(min); + for (i = ab = 1, ref3 = num - 1; 1 <= ref3 ? ab <= ref3 : ab >= ref3; i = 1 <= ref3 ? ++ab : --ab) { + centroids.push(min + (i / num) * (max - min)); + } + centroids.push(max); + while (repeat) { + for (j = ac = 0, ref4 = num - 1; 0 <= ref4 ? ac <= ref4 : ac >= ref4; j = 0 <= ref4 ? ++ac : --ac) { + clusterSizes[j] = 0; + } + for (i = ad = 0, ref5 = n - 1; 0 <= ref5 ? ad <= ref5 : ad >= ref5; i = 0 <= ref5 ? ++ad : --ad) { + value = values[i]; + mindist = Number.MAX_VALUE; + for (j = ae = 0, ref6 = num - 1; 0 <= ref6 ? ae <= ref6 : ae >= ref6; j = 0 <= ref6 ? ++ae : --ae) { + dist = abs(centroids[j] - value); + if (dist < mindist) { + mindist = dist; + best = j; + } + } + clusterSizes[best]++; + assignments[i] = best; + } + newCentroids = new Array(num); + for (j = af = 0, ref7 = num - 1; 0 <= ref7 ? af <= ref7 : af >= ref7; j = 0 <= ref7 ? ++af : --af) { + newCentroids[j] = null; + } + for (i = ag = 0, ref8 = n - 1; 0 <= ref8 ? ag <= ref8 : ag >= ref8; i = 0 <= ref8 ? ++ag : --ag) { + cluster = assignments[i]; + if (newCentroids[cluster] === null) { + newCentroids[cluster] = values[i]; + } else { + newCentroids[cluster] += values[i]; + } + } + for (j = ah = 0, ref9 = num - 1; 0 <= ref9 ? ah <= ref9 : ah >= ref9; j = 0 <= ref9 ? ++ah : --ah) { + newCentroids[j] *= 1 / clusterSizes[j]; + } + repeat = false; + for (j = ai = 0, ref10 = num - 1; 0 <= ref10 ? ai <= ref10 : ai >= ref10; j = 0 <= ref10 ? ++ai : --ai) { + if (newCentroids[j] !== centroids[i]) { + repeat = true; + break; + } + } + centroids = newCentroids; + nb_iters++; + if (nb_iters > 200) { + repeat = false; + } + } + kClusters = {}; + for (j = aj = 0, ref11 = num - 1; 0 <= ref11 ? aj <= ref11 : aj >= ref11; j = 0 <= ref11 ? ++aj : --aj) { + kClusters[j] = []; + } + for (i = ak = 0, ref12 = n - 1; 0 <= ref12 ? ak <= ref12 : ak >= ref12; i = 0 <= ref12 ? ++ak : --ak) { + cluster = assignments[i]; + kClusters[cluster].push(values[i]); + } + tmpKMeansBreaks = []; + for (j = al = 0, ref13 = num - 1; 0 <= ref13 ? al <= ref13 : al >= ref13; j = 0 <= ref13 ? ++al : --al) { + tmpKMeansBreaks.push(kClusters[j][0]); + tmpKMeansBreaks.push(kClusters[j][kClusters[j].length - 1]); + } + tmpKMeansBreaks = tmpKMeansBreaks.sort(function(a, b) { + return a - b; + }); + limits.push(tmpKMeansBreaks[0]); + for (i = am = 1, ref14 = tmpKMeansBreaks.length - 1; am <= ref14; i = am += 2) { + if (!isNaN(tmpKMeansBreaks[i])) { + limits.push(tmpKMeansBreaks[i]); + } + } + } + return limits; + }; + + hsi2rgb = function(h, s, i) { + + /* + borrowed from here: + http://hummer.stanford.edu/museinfo/doc/examples/humdrum/keyscape2/hsi2rgb.cpp + */ + var args, b, g, r; + args = unpack(arguments); + h = args[0], s = args[1], i = args[2]; + h /= 360; + if (h < 1 / 3) { + b = (1 - s) / 3; + r = (1 + s * cos(TWOPI * h) / cos(PITHIRD - TWOPI * h)) / 3; + g = 1 - (b + r); + } else if (h < 2 / 3) { + h -= 1 / 3; + r = (1 - s) / 3; + g = (1 + s * cos(TWOPI * h) / cos(PITHIRD - TWOPI * h)) / 3; + b = 1 - (r + g); + } else { + h -= 2 / 3; + g = (1 - s) / 3; + b = (1 + s * cos(TWOPI * h) / cos(PITHIRD - TWOPI * h)) / 3; + r = 1 - (g + b); + } + r = limit(i * r * 3); + g = limit(i * g * 3); + b = limit(i * b * 3); + return [r * 255, g * 255, b * 255, args.length > 3 ? args[3] : 1]; + }; + + rgb2hsi = function() { + + /* + borrowed from here: + http://hummer.stanford.edu/museinfo/doc/examples/humdrum/keyscape2/rgb2hsi.cpp + */ + var b, g, h, i, min, r, ref, s; + ref = unpack(arguments), r = ref[0], g = ref[1], b = ref[2]; + TWOPI = Math.PI * 2; + r /= 255; + g /= 255; + b /= 255; + min = Math.min(r, g, b); + i = (r + g + b) / 3; + s = 1 - min / i; + if (s === 0) { + h = 0; + } else { + h = ((r - g) + (r - b)) / 2; + h /= Math.sqrt((r - g) * (r - g) + (r - b) * (g - b)); + h = Math.acos(h); + if (b > g) { + h = TWOPI - h; + } + h /= TWOPI; + } + return [h * 360, s, i]; + }; + + chroma.hsi = function() { + return (function(func, args, ctor) { + ctor.prototype = func.prototype; + var child = new ctor, result = func.apply(child, args); + return Object(result) === result ? result : child; + })(Color, slice.call(arguments).concat(['hsi']), function(){}); + }; + + _input.hsi = hsi2rgb; + + Color.prototype.hsi = function() { + return rgb2hsi(this._rgb); + }; + + interpolate_hsx = function(col1, col2, f, m) { + var dh, hue, hue0, hue1, lbv, lbv0, lbv1, res, sat, sat0, sat1, xyz0, xyz1; + if (m === 'hsl') { + xyz0 = col1.hsl(); + xyz1 = col2.hsl(); + } else if (m === 'hsv') { + xyz0 = col1.hsv(); + xyz1 = col2.hsv(); + } else if (m === 'hsi') { + xyz0 = col1.hsi(); + xyz1 = col2.hsi(); + } else if (m === 'lch' || m === 'hcl') { + m = 'hcl'; + xyz0 = col1.hcl(); + xyz1 = col2.hcl(); + } + if (m.substr(0, 1) === 'h') { + hue0 = xyz0[0], sat0 = xyz0[1], lbv0 = xyz0[2]; + hue1 = xyz1[0], sat1 = xyz1[1], lbv1 = xyz1[2]; + } + if (!isNaN(hue0) && !isNaN(hue1)) { + if (hue1 > hue0 && hue1 - hue0 > 180) { + dh = hue1 - (hue0 + 360); + } else if (hue1 < hue0 && hue0 - hue1 > 180) { + dh = hue1 + 360 - hue0; + } else { + dh = hue1 - hue0; + } + hue = hue0 + f * dh; + } else if (!isNaN(hue0)) { + hue = hue0; + if ((lbv1 === 1 || lbv1 === 0) && m !== 'hsv') { + sat = sat0; + } + } else if (!isNaN(hue1)) { + hue = hue1; + if ((lbv0 === 1 || lbv0 === 0) && m !== 'hsv') { + sat = sat1; + } + } else { + hue = Number.NaN; + } + if (sat == null) { + sat = sat0 + f * (sat1 - sat0); + } + lbv = lbv0 + f * (lbv1 - lbv0); + return res = chroma[m](hue, sat, lbv); + }; + + _interpolators = _interpolators.concat((function() { + var len, o, ref, results; + ref = ['hsv', 'hsl', 'hsi', 'hcl', 'lch']; + results = []; + for (o = 0, len = ref.length; o < len; o++) { + m = ref[o]; + results.push([m, interpolate_hsx]); + } + return results; + })()); + + interpolate_num = function(col1, col2, f, m) { + var n1, n2; + n1 = col1.num(); + n2 = col2.num(); + return chroma.num(n1 + (n2 - n1) * f, 'num'); + }; + + _interpolators.push(['num', interpolate_num]); + + interpolate_lab = function(col1, col2, f, m) { + var res, xyz0, xyz1; + xyz0 = col1.lab(); + xyz1 = col2.lab(); + return res = new Color(xyz0[0] + f * (xyz1[0] - xyz0[0]), xyz0[1] + f * (xyz1[1] - xyz0[1]), xyz0[2] + f * (xyz1[2] - xyz0[2]), m); + }; + + _interpolators.push(['lab', interpolate_lab]); + +}).call(this); \ No newline at end of file diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index edc2028f..768367c3 100755 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -14,27 +14,28 @@ - +
- - + + - + {% for trait in traits %} - + {% endfor %} {% for trait in traits %} - + {% for result in corr_results[loop.index-1] %} {% if result[0].name == trait.name %} - + {% else %} - + + {% endif %} {% endfor %} @@ -64,6 +65,7 @@ + diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index d44fd2d4..b2d17b62 100755 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -22,8 +22,19 @@ and analysis page.

+
+ + + + + + + +
+
+
-
Spearman Rank Correlation (rho)Spearman Rank Correlation (rho)
P e a r s o n     rP e a r s o n     r Trait{{ loop.index }}Trait{{ loop.index }}
Trait {{ loop.index }}: {{ trait.dataset.name }}::{{ trait.name }}Trait {{ loop.index }}: {{ trait.dataset.name }}::{{ trait.name }}n
{{ result[2] }}		n
{{ result[2] }}		{{ '%0.3f' % result[1] }}
{{ result[2] }}		{{ '%0.3f' % result[1] }}
{{ result[2] }}
+
@@ -79,7 +90,7 @@ {% for trait in correlation_results %} -
+ {{ loop.index }} @@ -141,6 +152,8 @@ {% endblock %} {% block js %} + + @@ -202,7 +215,7 @@ $(document).ready( function () { - $('#corr_results tr').click(function(event) { + $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox') { $(':checkbox', this).trigger('click'); } @@ -213,7 +226,7 @@ {% if target_dataset.type == "ProbeSet" %} - $('#corr_results').dataTable( { + $('#trait_table').dataTable( { "columns": [ { "type": "natural" }, { "type": "natural" }, @@ -241,11 +254,11 @@ "paging": false } ); - var table = $('#corr_results').DataTable(); + var table = $('#trait_table').DataTable(); new $.fn.dataTable.FixedHeader( table ); {% elif target_dataset.type == "Publish" %} - $('#corr_results').dataTable( { + $('#trait_table').dataTable( { "columns": [ { "type": "natural" }, { "type": "natural" }, @@ -274,7 +287,7 @@ "paging": false } ); {% elif target_dataset.type == "Geno" %} - $('#corr_results').dataTable( { + $('#trait_table').dataTable( { "columns": [ { "type": "natural" }, { "type": "natural" }, diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 5b4dea33..f29b907d 100755 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -224,12 +224,6 @@ console.time("Creating table"); {% if dataset.type == 'ProbeSet' %} - jQuery.fn.dataTableExt.afnFiltering.push( - function( oSettings, aData, iDataIndex ) { - return filtering( oSettings, aData, iDataIndex, 7 ); - } - ); - $('#trait_table').DataTable( { "columns": [ { "type": "natural" }, @@ -243,6 +237,7 @@ { "type": "natural", "width": "15%" }, { "type": "natural" } ], + "order": [[1, "asc" ]], "buttons": [ 'csv' ], @@ -268,6 +263,7 @@ { "type": "natural", "width": "15%"}, { "type": "natural" } ], + "order": [[1, "asc" ]], "buttons": [ 'csv' ], @@ -288,6 +284,7 @@ { "type": "natural" }, { "type": "natural", "width": "40%"} ], + "order": [[1, "asc" ]], "buttons": [ 'csv' ], diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 65b9d08e..3203c0c4 100755 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -72,7 +72,7 @@ - + {% if this_trait.dataset.type == 'ProbeSet' %}
@@ -93,6 +93,7 @@
+ {% endif %}
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