spond · March 10, 2016 18:38
diff --git a/README.md b/README.md
diff --git a/g134_orf2overlap.fas.fubar.csv b/g134_orf2overlap.fas.fubar.csv
diff --git a/g134_orf3overlap.fas.fubar.csv b/g134_orf3overlap.fas.fubar.csv
diff --git a/hev_g134.fas.fubar.csv b/hev_g134.fas.fubar.csv
diff --git a/index.html b/index.html
 <!DOCTYPE html>
 <meta charset="utf-8">
 <style>
    body {
        font: 20px sans-serif;
    }
    
    .axis path,
    .axis line {
        fill: none;
        stroke: #000;
        shape-rendering: crispEdges;
    }
    
    .area {
        fill: #ddd;
        stroke: #444;
        stroke-width: 0.5px;
        fill-opacity: 0.33;
    }
    
    .line {
        fill: none;
        stroke: black;
        stroke-width: 0.5px;
    }

    .annotation-line {
        fill: none;
        stroke: #999;
        stroke-width: 2px;
    }

    .annotation-text {
        font: 20px sans-serif;
        text-anchor: middle;
        fill: #999;
    }
    
 </style>

 <body>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
    <script>
        var base_line = 20;

        var margin = {
                top: 40,
                right: 20,
                bottom: 3 * base_line,
                left: 2 * base_line
            },
            width = 1500 - margin.left - margin.right,
            height = 600 - margin.top - margin.bottom;

        function plot_some_data(plot_data, title, container, splitter, y_domain, annotator) {
            /* 
                plot_data -- the FUBAR data to plot; generated by load_file 
                title -- the title of the plot
                container -- the DOM element where the SVG with this plot will go
                splitter -- NULL (single color plot/no legend), or an array of the form
                            [ filter function (on codon indices),
                              fill color,
                              stroke color]
                              
                annotator -- NULL (no region annotation), or an array of entries like this
                            [ start_codon, end_codon, y-coordinate, label, label above or below line ]
            */
            
        
            var x = d3.scale.linear()
                .range([0, width]);

            var y = d3.scale.linear()
                .range([height, 0]);

            var xAxis = d3.svg.axis()
                .scale(x)
                .orient("bottom");

            var yAxis = d3.svg.axis()
                .scale(y)
                .orient("left");

            /* step-plot generator*/

            var area = d3.svg.area()
                .x(function(d) {
                    return x(d.codon);
                })
                .y0(function(d) {
                    return y(0);
                })
                .y1(function(d) {
                    return y(d.value);
                }).
            interpolate('step');


            var svg = container.append("svg").style("display", "table-cell")
                .attr("width", width + margin.left + margin.right)
                .attr("height", height + margin.top + margin.bottom)
                .append("g")
                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
            
            /* set the domain for the codons */

            x.domain(d3.extent(plot_data, function(d) {
                return d.codon;
            })).clamp (true);

            /* set user-specified domain (for beta-alpha), 
               or auto-detect one*/
                
            if (y_domain) {
                y.domain (y_domain).clamp (true);
            } else {
                y.domain(d3.extent(plot_data, function(d) {
                    return d.value;
                }));
            
                var symmetrize = d3.min (y.domain().map (function (d) {return Math.abs (d);}))*1.25;
                y.domain ([-symmetrize,symmetrize]).clamp(true);
            }

            /* determine if the plot needs to be partitioned into regions 
               if so, draw a separate path for each block
            */

            if (splitter) {
            
                splitter.forEach(function(d) {
                    svg.append("path").datum(plot_data.filter(d[0]))
                        .attr("class", "area")
                        .attr("d", area)
                        .style("fill", d[1])
                        .style("stroke", d[2]);
                    
                });
            } else {
                svg.append("path")
                    .datum(plot_data)
                    .attr("class", "area")
                    .attr("d", area);
            }

            /* for points that have posterior probability of 0.95 or greater, 
               plot a circle on the x-axis 
            */    
            
            plot_data.forEach (function (d) {
                if (d.pp >= 0.95) {
                    svg.append ("circle").attr ("cx", x(d.codon)).attr ("cy", y(0)).attr ("r", "5");
                }
            });

 
            /* handle annotation is provided
            */
            
            if (annotator) {
                annotator.forEach(function(d) {
                    svg.append("line")
                        .attr("class", "annotation-line")
                        .attr("x1", x(d[0]))
                        .attr("x2", x(d[1]))
                        .attr("y1", y(d[2]))
                        .attr("y2", y(d[2]));

                    for (i = 0; i < 2; i++) {
                        svg.append("line")
                            .attr("class", "annotation-line")
                            .attr("x1", x(d[i]))
                            .attr("x2", x(d[i]))
                            .attr("y1", y(d[2])-5)
                            .attr("y2", y(d[2])+5);
                    }
                        
                    svg.append ("text")
                        .attr("class", "annotation-text")
                        .attr("x", x(d[4]))
                        .attr("y", y(d[2]))
                        .attr("dy", d[5] ? "1.25em" : "-0.5em")
                        .text (d[3]);
                    
                });            
            }
           
             /* x-axis */
            svg.append("g")
                .attr("class", "x axis")
                .attr("transform", "translate(0," + height + ")")
                .call(xAxis)
                .append("text")
                .attr("x", width)
                .attr("dy", "+2.5em")
                .style("text-anchor", "end")
                .text("Codon");
                
            

           /* y-axis*/
            svg.append("g")
                .attr("class", "y axis")
                .call(yAxis)
                .append("text")
                .attr("transform", "rotate(-90)")
                .attr("y", 6)
                .attr("dy", ".71em")
                .style("text-anchor", "end")
                .text("\u03B2-\u03B1"); // beta - alpha

            /* plot title */
            if (title) {
                svg.append("text").text(title).style("font-size", "24px").attr("dx", "2em").attr("dy", "-0.1em");
            }
        }

        function load_file(list, index) {
            d3.csv(list[index][0], function(error, data) {
                if (error) throw error;

                var data_to_plot = [];
                var container_div = d3.select("body").append("div");


                fubar_info = [];

                data_to_plot.push([list[index][0], data.map(function(d) {
                    return {
                        "codon": +d["Codon"],
                        "value": +d["beta-alpha"],
                        "pp": +d["Prob[alpha<beta]"]
                    };
                })]);


                data_to_plot.forEach(function(d) {
                    plot_some_data(d[1], list[index][1], container_div, list[index][2], list[index][3], list[index][4]);
                });

                if (index + 1 < list.length) {
                    load_file(list, index + 1);
                }

            });
        }

        /* the first argument to load_file is an array with the following entries (arrays themselves)
            [ 
              URL for the file,
              label for the plot (can be null),
              plot splitter      (see plot_some_data),
              y-axis range       (can be null to auto-detect),
              annotator          (see plot_some_data, can be null)
            ]
        */
        
        load_file([
            ["hev_g134.fas.fubar.csv", "Full genome", [
                [function(d) {
                    return d.codon < 708;
                }, "#1f77b4", "#1f77b4"],
                [function(d) {
                    return d.codon >= 708 && d.codon < 898;
                }, "#d62728", "#d62728"],
                [function(d) {
                    return d.codon > 898 && d.codon < 1815;
                }, "#1f77b4", "#1f77b4"],
                 [function(d) {
                    return d.codon >= 1815 + 108;
                }, "#ff7f0e", "#ff7f0e"],
                [function(d) {
                    return d.codon >= 1815 && d.codon < 1815 + 108;
                }, "#2ca02c", "#2ca02c"]
            ],[-6,6], 
            [[1,1815,4,"ORF1",100,false],
             [708,898,-4,"HVR", (898+708)/2, true],
             [1815,10000,-4,"ORF2", 2000, true],
             [1815,1923,3,"ORF2/ORF3 overlap", 1869, false]
             ]
            ],
            ["g134_orf2overlap.fas.fubar.csv", "OFR2 overlap", null, [-6,6], null],
            ["g134_orf3overlap.fas.fubar.csv", "OFR3 overlap", null, [-6,6], null]
        ], 0);

        //d3.json("coverages-csf.json", function(error, data) {
    </script>
diff --git a/thumbnail.png b/thumbnail.png
Codon	alpha	beta	beta-alpha	Prob[alpha<beta]	Prob[alpha>beta]	BayesFactor	PSRF	Neff
1	0.5360047914952702	0.8600505521021546	0.3240457606068844	0.7087171547636242	0.2270132561617492	3.186818585295081	1.015836088083528	156.717838425269
2	0.2229004541459718	0.4172862068318389	0.1943857526858671	0.7004511725333298	0.2246887882355206	3.062735884015785	1.001680579337282	1149.596570477347
3	1.134225589228761	0.1806876466905644	-0.9535379425381968	0.04377003043572025	0.9381638466297002	0.05995339787388938	1.007089809199877	332.973612109066
4	0.2266831387149143	0.701052241147899	0.4743691024329847	0.8695617861500475	0.09576978910542519	8.731621609396969	1.010945366915377	222.0744845517508
5	0.2374160074458446	1.34541314848286	1.107997141037015	0.9784170663139353	0.01251900929520794	59.3762611702902	1.015604267611803	158.9195004937848
6	3.060247686018167	0.1415996542806216	-2.918648031737546	0.0001880135556411685	0.9995973052493385	0.0002463032417386119	1.003160646574824	686.3268716337445
7	1.741238941891345	0.3280147331793301	-1.413224208712015	0.01674013636685385	0.972427979444235	0.02229923600701794	1.000730729771498	2033.843691810246
8	7.546078792912378	0.1577286652610893	-7.388350127651289	5.297457557350867e-13	0.9999999979714171	6.938519131723129e-13	1.005361324635488	430.0559886003197
9	0.3298906430008735	2.926618581870017	2.596727938869143	0.9997595858456727	3.78560444489222e-07	5446.717467145242	1.001659097705371	1160.996318765202
10	0.3045815120799495	2.219148171537015	1.914566659457066	0.9909171567386295	0.004198001670683046	142.8942759721795	1.005773390530661	402.0552538340809
11	0.3907757107788584	0.8428225623500183	0.4520468515711599	0.8336098871671765	0.1247856276719875	6.56197611105719	1.015362091436453	161.2882471768085
12	0.2336675590788168	1.064804058128716	0.8311364990498993	0.9660244645618873	0.02133053246678237	37.24098159552432	1.018521582152033	135.1248435142318
13	7.821335752827073	0.1591980900991492	-7.662137662727924	3.488053743671349e-14	0.9999999989859025	4.568593022391851e-14	1.004461793848888	507.3384482247688
14	0.2074301881334885	0.1856981424372444	-0.0217320456962441	0.3787322873212047	0.4520657325664098	0.7984594239765125	1.006463848463448	362.5652508744116
15	3.338651167186176	0.06669562081631721	-3.271955546369858	0.06288768309766031	0.8582856537318024	0.08789683818714211	1.023275233673971	108.8629881784038
16	2.926083033811286	0.1438084001941377	-2.782274633617148	0.000540025458236096	0.998965709803235	0.0007076982664360581	1.003493674062944	629.4098198744045
17	0.24629713678954	0.1874181683919412	-0.05887896839759885	0.3489846542261695	0.4963958841901052	0.7021249543404829	1.007928302779014	300.2221261218131
18	0.3625776088014896	0.2185179390629168	-0.1440596697385728	0.311575066730296	0.5706819094441343	0.592796198322414	1.010568390259476	229.5098061828809
19	0.1979186705066627	0.1852816262935615	-0.01263704421310125	0.3863934881250546	0.440640625032236	0.8247819404414791	1.006108071246748	381.8829710468349
20	0.3611847984407818	0.1910796084499179	-0.170105189990864	0.2820419954397838	0.5951309518832968	0.5145339563411657	1.011486553924523	212.2180001641083
21	0.2752733362288638	1.265937214831677	0.9906638786028135	0.9420564494973765	0.03992043074716114	21.29468049210884	1.018394319395498	136.0095559395731
22	1.17904018194296	0.5261982400264926	-0.6528419419164677	0.1396819182264099	0.8084188659647555	0.2126573726490096	1.002407087207378	863.2520702805986
23	0.4180591230113387	0.1444370184401033	-0.2736221045712354	0.2089621657664651	0.6700210914522543	0.3459949096159362	1.014752474261368	167.5839804626631
24	0.3778453513330117	0.7989495795394411	0.4211042282064295	0.8005095835523155	0.1554320150007333	5.255860174767001	1.016876117251511	147.5634216941471
25	0.2254437971849968	0.4964131727000353	0.2709693755150384	0.7749110505688708	0.1686383855584739	4.509173896689897	1.00439052456547	514.676931474384
26	0.5306847523728295	0.2505301319788348	-0.2801546203939947	0.1933591446866402	0.7497136200404049	0.3139668573098298	1.008864223315459	270.5923007255892
27	1.925509185133732	0.1930868147643429	-1.732422370369389	0.01146343411600203	0.9820207975968851	0.01518872451119538	1.00296874839446	724.086798019288
28	2.926710279736979	0.4315273461423226	-2.495182933594656	0.002618865730969115	0.9938838103947709	0.003439152135376218	1.000919740970253	1763.59979524961
29	2.273782763632842	0.1832349407398954	-2.090547822892947	0.005185290464248512	0.9912675941335998	0.006827004597098942	1.002954939841862	726.9656871887445
30	0.363503357623676	0.2389069448065604	-0.1245964128171156	0.3326199282910612	0.5531762260464835	0.6527912666105403	1.009978589253578	242.2160861450159
31	1.0667759760589	0.4934439328635774	-0.5733320431953222	0.1947409131882241	0.7509541500352873	0.3167530987272744	1.004156965822205	540.3002369943461
32	0.2520400651239306	0.2087804974497151	-0.04325956767421554	0.3711340043371304	0.481973465400825	0.7729865543763177	1.007378788811975	320.8988345298553
33	0.291977840578174	0.6954992776687912	0.4035214370906172	0.8402043094797296	0.1216423875233631	6.886826567634351	1.017025423963462	146.338404850169
34	0.5398014481680726	0.5622593231251236	0.02245787495705098	0.4751892879636559	0.4519664578474039	1.18594146858423	1.00841828560166	283.9343620657872
35	0.4854986517784107	1.012360025442365	0.5268613736639546	0.7902989560385557	0.1577410430216379	4.936170133213706	1.017792972959811	140.3565518155483
36	0.5560588261995686	4.274793221232256	3.718734395032688	0.9987981152641057	6.602590267297919e-06	1088.464323542594	1.000755933284077	1993.108758691424
37	0.2682054141863505	0.7344567660330553	0.4662513518467049	0.844173474762847	0.117902823332897	7.095608079934988	1.013938924496186	176.813961814521
38	0.2733703845920231	3.512531253790756	3.239160869198733	0.999805077951468	6.102859758914871e-05	6718.211553625666	1.004149904557443	541.1150021977361
39	0.2095691853234943	0.2327011168181821	0.02313193149468781	0.4354738341450791	0.4111078941308863	1.010362672644726	1.005058385411552	453.2893083684243
40	0.2575619450586777	0.08223277991951523	-0.1753291651391625	0.187164748560672	0.6287861923400472	0.3015927028107434	1.015350626707865	161.4021792222722
41	3.566782557610608	0.1547921158599846	-3.411990441750623	0.1308282289535814	0.7989824182863913	0.1971492610865827	1.019701395024858	127.4536774674216
42	0.2244172443339378	0.5286713796285019	0.304254135294564	0.7716997789811298	0.1703393531906043	4.427324433589489	1.002154713555492	944.9575264525895
43	0.2610432481341126	0.1217806049580454	-0.1392626431760672	0.2484382551057066	0.5827551887558524	0.4329653172553982	1.011883845111737	205.5306052009003
44	1.084150300411859	0.1704749616180725	-0.9136753387937862	0.04102455808066806	0.9414311849095892	0.0560319491313295	1.007416595735069	319.3843122071199
45	0.2275020815750676	0.787627551189124	0.5601254696140564	0.9201607041604373	0.05667828215676031	15.09545781710552	1.017935782553228	139.2985355108372
46	0.2185302630973374	0.1203961751812047	-0.09813408791613262	0.275228938927503	0.5367752310404645	0.4973848533191358	1.010321632128656	234.6572805397458
47	0.4779414857350652	0.3466778644857203	-0.1312636212493449	0.3171455585222806	0.5960875385674889	0.6083167842728912	1.004242403408376	530.6342841216981
48	0.4180591230113387	0.1444370184401033	-0.2736221045712354	0.2089621657664651	0.6700210914522543	0.3459949096159362	1.014752474261368	167.5839804626631
49	0.24629713678954	0.1874181683919412	-0.05887896839759885	0.3489846542261695	0.4963958841901052	0.7021249543404829	1.007928302779014	300.2221261218131
50	0.2575619450586777	0.08223277991951523	-0.1753291651391625	0.187164748560672	0.6287861923400472	0.3015927028107434	1.015350626707865	161.4021792222722
51	1.499442126800243	0.2164902892376079	-1.282951837562635	0.02714611756075144	0.9602536723490678	0.03654764631021916	1.002773636245342	767.0177349348645
52	0.2709990302346293	0.6254076755567257	0.3544086453220964	0.8163368097096662	0.140753805845473	5.821656277294287	1.014249800834072	173.1667653201171
53	0.24629713678954	0.1874181683919412	-0.05887896839759885	0.3489846542261695	0.4963958841901052	0.7021249543404829	1.007928302779014	300.2221261218131
54	0.2355212017515021	0.2549187835725329	0.01939758182103077	0.5320655521857313	0.3590261050212048	1.489290532180955	1.00436645348201	517.2040495240491
55	0.2082112179851247	0.07509993654829128	-0.1331112814368334	0.2022340154911447	0.5842016979566186	0.3320305116594275	1.014384263172917	171.6364565231677
56	0.2177073134209214	0.1084960861861787	-0.1092112272347428	0.2563714890994047	0.5504592698717325	0.4515574353786624	1.011218401017941	216.9879993935697
57	0.1979186705066627	0.1852816262935615	-0.01263704421310125	0.3863934881250546	0.440640625032236	0.8247819404414791	1.006108071246748	381.8829710468349
58	0.2406628010847118	0.1041296858780416	-0.1365331152066702	0.2337102242492458	0.5825752049228685	0.3994698305586689	1.012514990450796	195.7463694013921
59	0.8373206915068032	0.0778777464599439	-0.7594429450468593	0.01045568094825139	0.9799337652484106	0.01383937179413383	1.011533926093662	211.3974222851199
60	0.24629713678954	0.1874181683919412	-0.05887896839759885	0.3489846542261695	0.4963958841901052	0.7021249543404829	1.007928302779014	300.2221261218131
61	3.830553906689186	0.07716434960038464	-3.753389557088802	1.642779779192077e-05	0.9999660908602459	2.151720152238624e-05	1.010912853944726	222.6964007735378
62	0.7027340964303159	0.2333731249035514	-0.4693609715267645	0.1051539016898992	0.8596459515702073	0.1539133698888538	1.005555682025697	416.3741991600706
63	1.295730476577964	1.068672674230152	-0.2270578023478116	0.3811997207879543	0.5030567791894577	0.8068659288736165	1.00501231147178	457.0465814452448
64	1.169304222905424	0.1312031644093412	-1.038101058496082	0.01467555629945551	0.9771352513486498	0.01950808414884015	1.005286482396398	435.569608142857
65	1.470850937068388	0.3138021299439555	-1.157048807124432	0.0306469336763527	0.9534169990901467	0.04140991549921118	1.000577787626389	2321.888045100238
66	1.000177425673683	1.717630596425833	0.7174531707521501	0.6926141576008339	0.1984463252743207	2.951255490339056	1.006740691287018	348.8467726803926
67	1.209307149050195	2.683737965053075	1.47443081600288	0.8181685828200832	0.03738092976210491	5.893498529091667	1.000334272463477	2998.425852463502
68	1.834652672001354	0.7184779837752527	-1.116174688226101	0.1138218344258341	0.8276746302533651	0.1682301528954811	1.002710076703139	782.1297728297956
69	0.3145523591089464	3.868787296035804	3.554234936926858	0.9998159505160749	1.658541078993905e-05	7115.161484155487	1.000445272907978	2646.817072169971
70	0.363503357623676	0.2389069448065604	-0.1245964128171156	0.3326199282910612	0.5531762260464835	0.6527912666105403	1.009978589253578	242.2160861450159
71	0.2407113822716934	1.653104451136892	1.412393068865199	0.9771306713101874	0.0145424031271857	55.96268375829581	1.016392759823257	151.6777609545373
72	0.2142670691919318	0.5425997806546153	0.3283327114626836	0.7892100300512246	0.1552697221006506	4.903903984420971	1.00191472436229	1038.494983998575
73	0.5124763462117307	3.153479243970223	2.641002897758492	0.9983628721651086	0.0005153297039714191	798.7394473476342	1.000657249528257	2162.731667946293
74	1.016926877100077	0.2185954206874102	-0.7983314564126672	0.05050435274679797	0.9294004343657585	0.06966828755846978	1.002842360786096	751.3243428586792
75	0.2276093804313563	0.7995629336758906	0.5719535532445343	0.910791189082697	0.06402930362170639	13.37243126473216	1.016947201993463	146.9775776840641
76	2.653903259823172	0.4992899049757604	-2.154613354847411	0.01093208639408371	0.9774351945570089	0.01447692239375662	1.003027841882372	712.0212212548095
77	6.375078074372523	0.3287173120419669	-6.046360762330557	0.0001442325533084325	0.9997172500623265	0.0001889405781454544	1.001321996040446	1375.092309507602
78	5.573407070134705	0.3994652273016629	-5.173941842833042	3.451815117820566e-05	0.9997794944655798	4.521284357612121e-05	1.001064766082793	1600.507208907785
79	0.5564912981499427	5.487657719080235	4.931166420930293	0.9993897676705139	9.839350884510346e-06	2145.057757456325	1.000601214651876	2272.578057949589
80	7.197830750629794	0.193033117564145	-7.004797633065649	9.409671003528998e-09	0.9999986241178487	1.232462595286389e-08	1.004112159842029	545.5124910013963
81	0.887849964148625	0.2048984147945204	-0.6829515493541047	0.05061540192425877	0.9288625018026766	0.06982964146714431	1.00268817421193	787.4769398429315
82	4.249213754570963	0.1099438147987824	-4.139269939772181	1.068858236340981e-05	0.9999737354678235	1.399987165950198e-05	1.007321084965238	323.2386444171123
83	6.033816862968067	0.196548196942385	-5.837268666025682	5.169381440423868e-06	0.9999526390548261	6.770802229332114e-06	1.004353479996537	518.5764747632775
84	0.7609963269220931	0.1311046265796399	-0.6298917003424532	0.03477671031361935	0.9461789274584854	0.04719109010730906	1.008809268670049	272.1674394730343
85	0.7937492476208752	1.563033693285919	0.7692844456650438	0.7402303227477459	0.1810218834961827	3.732310108132312	1.007985367343536	298.2284347452314
86	3.566782557610608	0.1547921158599846	-3.411990441750623	0.1308282289535814	0.7989824182863913	0.1971492610865827	1.019701395024858	127.4536774674216
87	4.379038894366089	0.1667645766682435	-4.212274317697846	2.098076527512474e-05	0.9999158345954628	2.748082340099276e-05	1.003627259437128	609.1601133509571
88	0.8941052396901131	0.1332327621102857	-0.7608724775798275	0.02986375734944221	0.9540482753544017	0.04031911798900342	1.008774198881536	273.1823854877392
89	3.854038599593019	0.1201134680829092	-3.73392513151011	0.001118839466944207	0.9981636663338623	0.001467078186417012	1.01000963067689	241.5117955129581
90	0.2628776180864682	0.360964285324699	0.09808666723823078	0.6061952775252177	0.3086292518934815	2.016187570806282	1.002810934054192	758.419863414579
91	0.8754548922214568	0.538644418531409	-0.3368104736900478	0.3244491688236954	0.608459146816074	0.6290540133668634	1.007328632016057	322.9306614785383
92	0.2472295872209744	0.2040932071512478	-0.04313638006972659	0.3691975190498188	0.4811462843026571	0.7665927108873145	1.007356133247186	321.8133874985928
93	0.2644394783592831	0.4638205095468256	0.1993810311875425	0.6882477490246213	0.2429243149002895	2.891575297634685	1.002841915301999	751.4239917519481
94	0.7105946502865079	2.993324745210836	2.282730094924328	0.9907692161462929	0.0006436305121449263	140.5831359628719	0.9999011305168852	6231.0772102213
95	0.7739278239281717	2.855722568949014	2.081794745020842	0.9762004880416955	0.007584592162454655	53.72423910906463	1.000545107513539	2394.366621923158
96	0.5636105764224808	2.927665613177196	2.364055036754715	0.9955734313879667	0.001216077550508499	294.5814545387653	0.9997614699416173	9555.728021093348
97	0.7925654485024725	7.02794661642657	6.235381167924098	0.9992297587306359	1.285549372136734e-06	1699.174099471142	1.00129994586287	1391.890698470037
98	3.627042166446832	0.1667673580667225	-3.460274808380109	4.478314379591258e-05	0.9998460199153228	5.865882126918546e-05	1.002641007767675	799.2451231006194
99	0.4692652658783387	0.2177477896040826	-0.251517476274256	0.1868274524491816	0.7510906223552528	0.3009243198033555	1.009252990052638	259.9562326563803
100	0.4467455071443048	0.6002043846965851	0.1534588775522803	0.5773458622564775	0.3504474586964209	1.789164353290016	1.008061297196656	295.6168476301922
101	0.2547306703068934	2.215941004945226	1.961210334638332	0.9942309763110833	0.002837519860109792	225.7273961614554	1.008110261463294	293.9571632816067
102	0.5555017343758376	2.349584850633009	1.794083116257172	0.9685304917761988	0.0167327866736244	40.31091405780442	1.004060263442026	551.6775855467755
103	0.4637021049357125	0.7603803588830158	0.2966782539473033	0.734427349677139	0.2050170326435006	3.622136377134126	1.017942570218036	139.2486564870985
104	0.7810141700369861	2.513075778791377	1.732061608754391	0.9392690359881269	0.02988225185137492	20.25718689138133	1.003586860289299	615.1444376600606
105	0.363503357623676	0.2389069448065604	-0.1245964128171156	0.3326199282910612	0.5531762260464835	0.6527912666105403	1.009978589253578	242.2160861450159
106	0.4783493164700957	0.2287982953855429	-0.2495510210845528	0.194045530584755	0.7444287629280592	0.3153497132317367	1.009148436690257	262.7323939635441
107	0.3781053009604317	0.6148917111850113	0.2367864102245796	0.7023034973224301	0.2425622259947774	3.089942535068199	1.013331530311036	184.4130102679601
108	0.3611847984407818	0.1910796084499179	-0.170105189990864	0.2820419954397838	0.5951309518832968	0.5145339563411657	1.011486553924523	212.2180001641083
	<!DOCTYPE html>
	<meta charset="utf-8">
	<style>
	body {
	font: 20px sans-serif;
	}

	.axis path,
	.axis line {
	fill: none;
	stroke: #000;
	shape-rendering: crispEdges;
	}

	.area {
	fill: #ddd;
	stroke: #444;
	stroke-width: 0.5px;
	fill-opacity: 0.33;
	}

	.line {
	fill: none;
	stroke: black;
	stroke-width: 0.5px;
	}

	.annotation-line {
	fill: none;
	stroke: #999;
	stroke-width: 2px;
	}

	.annotation-text {
	font: 20px sans-serif;
	text-anchor: middle;
	fill: #999;
	}

	</style>

	<body>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
	<script>
	var base_line = 20;

	var margin = {
	top: 40,
	right: 20,
	bottom: 3 * base_line,
	left: 2 * base_line
	},
	width = 1500 - margin.left - margin.right,
	height = 600 - margin.top - margin.bottom;

	function plot_some_data(plot_data, title, container, splitter, y_domain, annotator) {
	/*
	plot_data -- the FUBAR data to plot; generated by load_file
	title -- the title of the plot
	container -- the DOM element where the SVG with this plot will go
	splitter -- NULL (single color plot/no legend), or an array of the form
	[ filter function (on codon indices),
	fill color,
	stroke color]

	annotator -- NULL (no region annotation), or an array of entries like this
	[ start_codon, end_codon, y-coordinate, label, label above or below line ]
	*/


	var x = d3.scale.linear()
	.range([0, width]);

	var y = d3.scale.linear()
	.range([height, 0]);

	var xAxis = d3.svg.axis()
	.scale(x)
	.orient("bottom");

	var yAxis = d3.svg.axis()
	.scale(y)
	.orient("left");

	/* step-plot generator*/

	var area = d3.svg.area()
	.x(function(d) {
	return x(d.codon);
	})
	.y0(function(d) {
	return y(0);
	})
	.y1(function(d) {
	return y(d.value);
	}).
	interpolate('step');


	var svg = container.append("svg").style("display", "table-cell")
	.attr("width", width + margin.left + margin.right)
	.attr("height", height + margin.top + margin.bottom)
	.append("g")
	.attr("transform", "translate(" + margin.left + "," + margin.top + ")");

	/* set the domain for the codons */

	x.domain(d3.extent(plot_data, function(d) {
	return d.codon;
	})).clamp (true);

	/* set user-specified domain (for beta-alpha),
	or auto-detect one*/

	if (y_domain) {
	y.domain (y_domain).clamp (true);
	} else {
	y.domain(d3.extent(plot_data, function(d) {
	return d.value;
	}));

	var symmetrize = d3.min (y.domain().map (function (d) {return Math.abs (d);}))*1.25;
	y.domain ([-symmetrize,symmetrize]).clamp(true);
	}

	/* determine if the plot needs to be partitioned into regions
	if so, draw a separate path for each block
	*/

	if (splitter) {

	splitter.forEach(function(d) {
	svg.append("path").datum(plot_data.filter(d[0]))
	.attr("class", "area")
	.attr("d", area)
	.style("fill", d[1])
	.style("stroke", d[2]);

	});
	} else {
	svg.append("path")
	.datum(plot_data)
	.attr("class", "area")
	.attr("d", area);
	}

	/* for points that have posterior probability of 0.95 or greater,
	plot a circle on the x-axis
	*/

	plot_data.forEach (function (d) {
	if (d.pp >= 0.95) {
	svg.append ("circle").attr ("cx", x(d.codon)).attr ("cy", y(0)).attr ("r", "5");
	}
	});


	/* handle annotation is provided
	*/

	if (annotator) {
	annotator.forEach(function(d) {
	svg.append("line")
	.attr("class", "annotation-line")
	.attr("x1", x(d[0]))
	.attr("x2", x(d[1]))
	.attr("y1", y(d[2]))
	.attr("y2", y(d[2]));

	for (i = 0; i < 2; i++) {
	svg.append("line")
	.attr("class", "annotation-line")
	.attr("x1", x(d[i]))
	.attr("x2", x(d[i]))
	.attr("y1", y(d[2])-5)
	.attr("y2", y(d[2])+5);
	}

	svg.append ("text")
	.attr("class", "annotation-text")
	.attr("x", x(d[4]))
	.attr("y", y(d[2]))
	.attr("dy", d[5] ? "1.25em" : "-0.5em")
	.text (d[3]);

	});
	}

	/* x-axis */
	svg.append("g")
	.attr("class", "x axis")
	.attr("transform", "translate(0," + height + ")")
	.call(xAxis)
	.append("text")
	.attr("x", width)
	.attr("dy", "+2.5em")
	.style("text-anchor", "end")
	.text("Codon");



	/* y-axis*/
	svg.append("g")
	.attr("class", "y axis")
	.call(yAxis)
	.append("text")
	.attr("transform", "rotate(-90)")
	.attr("y", 6)
	.attr("dy", ".71em")
	.style("text-anchor", "end")
	.text("\u03B2-\u03B1"); // beta - alpha

	/* plot title */
	if (title) {
	svg.append("text").text(title).style("font-size", "24px").attr("dx", "2em").attr("dy", "-0.1em");
	}
	}

	function load_file(list, index) {
	d3.csv(list[index][0], function(error, data) {
	if (error) throw error;

	var data_to_plot = [];
	var container_div = d3.select("body").append("div");


	fubar_info = [];

	data_to_plot.push([list[index][0], data.map(function(d) {
	return {
	"codon": +d["Codon"],
	"value": +d["beta-alpha"],
	"pp": +d["Prob[alpha<beta]"]
	};
	})]);


	data_to_plot.forEach(function(d) {
	plot_some_data(d[1], list[index][1], container_div, list[index][2], list[index][3], list[index][4]);
	});

	if (index + 1 < list.length) {
	load_file(list, index + 1);
	}

	});
	}

	/* the first argument to load_file is an array with the following entries (arrays themselves)
	[
	URL for the file,
	label for the plot (can be null),
	plot splitter (see plot_some_data),
	y-axis range (can be null to auto-detect),
	annotator (see plot_some_data, can be null)
	]
	*/

	load_file([
	["hev_g134.fas.fubar.csv", "Full genome", [
	[function(d) {
	return d.codon < 708;
	}, "#1f77b4", "#1f77b4"],
	[function(d) {
	return d.codon >= 708 && d.codon < 898;
	}, "#d62728", "#d62728"],
	[function(d) {
	return d.codon > 898 && d.codon < 1815;
	}, "#1f77b4", "#1f77b4"],
	[function(d) {
	return d.codon >= 1815 + 108;
	}, "#ff7f0e", "#ff7f0e"],
	[function(d) {
	return d.codon >= 1815 && d.codon < 1815 + 108;
	}, "#2ca02c", "#2ca02c"]
	],[-6,6],
	[[1,1815,4,"ORF1",100,false],
	[708,898,-4,"HVR", (898+708)/2, true],
	[1815,10000,-4,"ORF2", 2000, true],
	[1815,1923,3,"ORF2/ORF3 overlap", 1869, false]
	]
	],
	["g134_orf2overlap.fas.fubar.csv", "OFR2 overlap", null, [-6,6], null],
	["g134_orf3overlap.fas.fubar.csv", "OFR3 overlap", null, [-6,6], null]
	], 0);

	//d3.json("coverages-csf.json", function(error, data) {
	</script>