30:Tb65,vegalite({ "data": {values: sliding_window}, "width": 400, "height": 400, "transform": [ {"filter": {"field": "CV", "range" : [0.0000001,5]}} ], "encoding" : { "x": { "field": "CV", "type": "quantitative", "scale": {"type": "pow", "exponent" : 1}, "axis":{ title : "CV (SRV)", titleFontSize: 20, labelFontSize: 20, format : "g" } }}, "layer": [ {"layer" : [ { mark: {"type": "line", "color" :"grey", "strokeWidth" : 5, "opacity" : 0.3}, "encoding": { "y": { //"aggregate": "count", "field": "KAPPA", "type": "quantitative", "axis":{ "orient": "right", "title" : "Cohen's kappa", grid : false, titleFontSize: 20, labelFontSize: 20, format : "g" } } } }]}, /*{"mark": "rule", "encoding": { "x": { "field": "CV", "type": "quantitative", "aggregate": "q1" }, "size": {"value": 2}, }},*/ { mark: {"type": "line", "color" :"grey", "strokeWidth" : 3, "opacity" : 0.7}, "encoding": { "y": { //"aggregate": "count", "field": "RATIO", "type": "quantitative", //"scale" : { // "domain": [0.75,1.5], //}, "axis":{ "orient": "left", "title" : "Detection rate ratio, BUSTED / BUSTED[S]", titleFontSize: 20, labelFontSize: 20, format : "g" } } } }, /*{ mark: {"type": "line", "color" :"#377eb8","strokeWidth" : 3,"opacity" : 0.7}, "encoding": { "y": { //"aggregate": "count", "orient": "left", "scale" : { "domain": [0,0.25], }, "field": "BUSTED_S", "type": "quantitative", "axis": null } } }, { mark: {"type": "line", "color" :"#4daf4a","strokeWidth" : 3,"opacity" : 0.7}, "encoding": { "y": { "orient": "left", "scale" : { "domain": [0,0.25], }, //"aggregate": "count", "field": "BOTH", "type": "quantitative", "axis": null } } },*/ {data: {values: [ {"label": "Detection Rate Ratio", "x": 1.4, "y": 1.45}, {"label": "Kappa", "x": 1.4, "y": 0.9} ]}, mark: {type: "text", align: "left", dx: 3, fontSize : 20, color : "black", }, encoding: { x: {field: "x", type: "quantitative"}, y: {field: "y", type: "quantitative", axis :null, "orient": "left", "scale" : { "domain": [0.75,1.5], }}, text: {field: "label", type: "nominal"} } } ], "resolve": {"scale": {"y": "independent"}} })31:T431,curves = { var x =_.map (_.filter (selectome, (d) => d.CV_SRV != "NA"), (d)=> { return [d.CV_SRV , d.BUSTED_SRV_P, d.BUSTED_P]; }); const pv = 0.05; x.sort ((d1,d2) => d1[0] - d2[0]); x[0][3] = (x[0][1] <= pv && x[0][2] <= pv) ? 1 : 0; x[0][4] = x[0][3] + (x[0][1] > pv && x[0][2] > pv ? 1 : 0); x[0][1] = x[0][1] <= pv ? 1 : 0; x[0][2] = x[0][2] <= pv ? 1 : 0; for (var i = 1; i < x.length; i++) { x[i][3] = (x[i][2] <= pv && x[i][1] <= pv ? 1 : 0) + x[i-1][3]; x[i][4] = x[i-1][4] + (x[i][1] > pv && x[i][2] > pv || x[i][1] <= pv && x[i][2] <= pv ? 1 : 0); x[i][1] = (x[i][1] <= pv ? 1 : 0) + x[i-1][1]; x[i][2] = (x[i][2] <= pv ? 1 : 0) + x[i-1][2]; } x = _.map (x, (d,i) => { var pe = d[1] * d[2] / (i+1) / (i+1) + ((i+1)-d[1]) * ((i+1)-d[2]) / (i+1) / (i+1); return { "CV" : d[0], "BUSTED_S" : d[1] / (i+1), "BUSTED" : d[2] / (i+1), "BOTH" : d[3] / (i+1), "RATIO" : d[2] / d[1], "KAPPA" : pe < 1 ? (d[4]/(i+1) - pe) / (1-pe) : 1 }}); return x; }32:[] 2e:{"title":"","cells":[{"id":680,"value":"md `## BUSTED vs BUSTED[S] performance of Selectome data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":782,"value":"viewof w_width = slider({\n min: 0.05,\n max: 0.5,\n value : 0.2,\n precision: 2,\n description: \"Sliding window size\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":796,"value":"viewof w_step = slider({\n min: 0.01,\n max: 0.2,\n value : 0.05,\n precision: 3,\n description: \"Sliding window step\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":8,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":4,"value":"vegalite = require(\"vega-embed@3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":162,"value":"d3 = require(\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":202,"value":"_.map (_.groupBy (_.map (selectome, (d)=> {\n if (d.CV_SRV < 0.001) {\n return [0, d.BUSTED_SRV_P, d.BUSTED_P];\n } \n if (d.CV_SRV < 0.2) {\n return [1, d.BUSTED_SRV_P, d.BUSTED_P];\n }\n if (d.CV_SRV < 0.5) {\n return [2, d.BUSTED_SRV_P, d.BUSTED_P];\n }\n if (d.CV_SRV < 1.0) {\n return [3, d.BUSTED_SRV_P, d.BUSTED_P];\n }\n if (d.CV_SRV < 5.0) {\n return [4, d.BUSTED_SRV_P, d.BUSTED_P];\n }\n return [5, d.BUSTED_SRV_P, d.BUSTED_P];\n}), (d) => d[0]), \n (d,i) => [i, d.length, _.filter (d, (e) => e[1] <= 0.05).length / d.length, _.filter (d, (e) => e[2] <= 0.05).length / d.length])\n ","pinned":true,"hidden":false,"mode":"ojs"},{"id":242,"value":"$31","pinned":true,"hidden":false,"mode":"ojs"},{"id":723,"value":"range_stats = (data, from, to) => {\n var x =_.map (_.filter (data, (d) => d.CV_SRV != \"NA\" && d.CV_SRV >= from && d.CV_SRV <= to), (d)=> {\n return [d.CV_SRV , d.BUSTED_SRV_P, d.BUSTED_P];\n });\n \n const pv = 0.05;\n var detection_busted = _.filter (x, (x) => x[2] <= pv).length / x.length;\n var detection_busteds = _.filter (x, (x) => x[1] <= pv).length / x.length;\n var agreed = _.filter (x, (x) => x[2] <= pv && x[1] <= pv || x[2] > pv && x[1] > pv).length / x.length;\n\n var pe = detection_busted * detection_busteds + (1-detection_busteds)*(1-detection_busted);\n \n return [x.length,detection_busted,detection_busteds, pe < 1 ? (agreed - pe) / (1 - pe) : 1];\n};","pinned":false,"hidden":false,"mode":"ojs"},{"id":573,"value":"sliding_window_generator = (step, slide) => _.filter(_.map (_.range (0, 3, slide), (d)=> {\n var range_info = range_stats (selectome, d, d + step);\n return {\n \"CV\" : d + step * 0.5,\n \"BUSTED\" : range_info[1],\n \"BUSTED_S\" : range_info[2],\n \"RATIO\" : range_info[2] > 0 ? range_info[1]/range_info[2] : 1,\n \"KAPPA\" : range_info[3],\n \"COUNT\" : range_info[0]\n };\n}), (d)=>d[\"COUNT\"] >= 10);","pinned":false,"hidden":false,"mode":"ojs"},{"id":780,"value":"sliding_window = sliding_window_generator (w_width, w_step)","pinned":true,"hidden":false,"mode":"ojs"},{"id":170,"value":"selectome = d3.csv (\"https://dl.dropbox.com/s/2vd6w7zv9glt5zl/selectome_8_28_18.csv\", d3.autoType)","pinned":true,"hidden":false,"mode":"ojs"},{"id":23,"value":"_=require ('lodash')","pinned":false,"hidden":false,"mode":"ojs"},{"id":786,"value":"import {slider} from \"@jashkenas/inputs\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":461,"value":"/*vegalite({\n \"data\": {values: selectome},\n \"width\": 600,\n \"height\": 600,\n \"transform\": [\n {\"filter\": {\"field\": \"CV_SRV\", \"range\" : [0.00,1.0]}},\n {\"filter\": {\"field\": \"BUSTED_SRV_treelength\", \"lte\" : 10}}\n\n ],\n \"layer\": [\n {\n mark: \"bar\",\n \"encoding\": {\n \"x\": {\n \"bin\": {step : 0.05},\n \"field\": \"CV_SRV\",\n \"type\": \"quantitative\",\n \"axis\":{\n \"title\" : \"CV (SRV)\",\n }\n },\n \"y\": {\n \"aggregate\": \"mean\",\n \"field\": \"Sequences\",\n \"type\": \"quantitative\",\n \"axis\":{\n \"title\" : \"Mean number of sequences\"\n }\n }\n }\n }]\n})*/","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}