2b:null 2c:["$","title",null,{"children":"SCAN: Location Compare for Variants | Zan | Observable"}] 31:T570,The following charts are designed to compare the prevalence of specific variants, ${textcolor(variantNames.get("Delta_156157"), variantColors.get("Delta_156157"))} (testing for del156/157/R158G), ${textcolor(variantNames.get("Del_143145"), variantColors.get("Del_143145"))} (testing for del143/145), ${textcolor(variantNames.get("BA_2_LPPA24S"), variantColors.get("BA_2_LPPA24S"))} (testing for LPPA24S), ${textcolor(variantNames.get("BA_4_ORF1a_Del_141143"), variantColors.get("BA_4_ORF1a_Del_141143"))} (testing for ORF1a_Del_141143), ${textcolor(variantNames.get("HV_6970_Del"), variantColors.get("HV_6970_Del"))} (testing for HV_6970_Del), ${textcolor(variantNames.get("BA_2_75_S_147E_S_152R"), variantColors.get("BA_2_75_S_147E_S_152R"))} (testing for BA_2_75_S_147E_S_152R), and ${textcolor(variantNames.get("XBB_bkpt"), variantColors.get("XBB_bkpt"))} (testing for BA_2_75_S_147E_S_152R) compared to ${textcolor('all variants of SARS-CoV-2', "black")} (testing for the N gene of SARS-CoV-2). Some charts will show the variant as a percent of all variants. Other charts will show the normalized values for the amount of delta-specific, omicron-specific, and N (all variants) RNA found in the samples from the wastewater plants. *[Note: This page is designed for use on non-mobile device. If using on mobile and having issues scrolling, try placing finger on far right side.]*32:Tac5,sidebysideratiocharts = html`

${textcolor(variantNames.get("Delta_156157"), variantColors.get("Delta_156157"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("Delta_156157", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("Del_143145"), variantColors.get("Del_143145"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("Del_143145", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("BA_2_LPPA24S"), variantColors.get("BA_2_LPPA24S"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("BA_2_LPPA24S", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("BA_4_ORF1a_Del_141143"), variantColors.get("BA_4_ORF1a_Del_141143"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("BA_4_ORF1a_Del_141143", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("HV_6970_Del"), variantColors.get("HV_6970_Del"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("HV_6970_Del", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("BA_2_75_S_147E_S_152R"), variantColors.get("BA_2_75_S_147E_S_152R"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("BA_2_75_S_147E_S_152R", smoothPoints, false, showLines, showPoints))}

${textcolor(variantNames.get("XBB_bkpt"), variantColors.get("XBB_bkpt"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("XBB_bkpt", smoothPoints, false, showLines, showPoints))}

`33:Tb21,faceted = html`

${textcolor(variantNames.get("Delta_156157"), variantColors.get("Delta_156157"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("Delta_156157", smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get("Del_143145"), variantColors.get("Del_143145"))} as a percent of all variants (N)

${addTooltips(variantPercentPlot("Del_143145", smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get(variantsToShow[2]), variantColors.get(variantsToShow[2]))} as a percent of all variants (N)

${addTooltips(variantPercentPlot(variantsToShow[2], smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get(variantsToShow[3]), variantColors.get(variantsToShow[3]))} as a percent of all variants (N)

${addTooltips(variantPercentPlot(variantsToShow[3], smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get(variantsToShow[4]), variantColors.get(variantsToShow[4]))} as a percent of all variants (N)

${addTooltips(variantPercentPlot(variantsToShow[4], smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get(variantsToShow[5]), variantColors.get(variantsToShow[5]))} as a percent of all variants (N)

${addTooltips(variantPercentPlot(variantsToShow[5], smoothPoints, true, showLinesFaceted, showPointsFaceted))}

${textcolor(variantNames.get(variantsToShow[6]), variantColors.get(variantsToShow[6]))} as a percent of all variants (N)

${addTooltips(variantPercentPlot(variantsToShow[6], smoothPoints, true, showLinesFaceted, showPointsFaceted))}

`34:T7ed,oneplant = html`

${textcolor('all variants (N)', "black")}; ${textcolor(variantNames.get("Delta_156157"), variantColors.get("Delta_156157"))}, ${textcolor(variantNames.get("Del_143145"), variantColors.get("Del_143145"))}, ${textcolor(variantNames.get("BA_2_LPPA24S"), variantColors.get("BA_2_LPPA24S"))}, ${textcolor(variantNames.get("BA_4_ORF1a_Del_141143"), variantColors.get("BA_4_ORF1a_Del_141143"))}, ${textcolor(variantNames.get("HV_6970_Del"), variantColors.get("HV_6970_Del"))}, ${textcolor(variantNames.get("BA_2_75_S_147E_S_152R"), variantColors.get("BA_2_75_S_147E_S_152R"))}, ${textcolor(variantNames.get("XBB_bkpt"), variantColors.get("XBB_bkpt"))}- all values are normalized by PMMoV ("fecal strength"), 5-day trimmed mean

${plotvariant("Delta_156157_PMMoV", variantColors.get("Delta_156157_PMMoV"), "circle", singlePlant)}

${plotvariant("Del_143145_PMMoV", variantColors.get("Del_143145_PMMoV"), "circle", singlePlant)}

${plotvariant("BA_2_LPPA24S_PMMoV", variantColors.get("BA_2_LPPA24S_PMMoV"), "circle", singlePlant)}

${plotvariant("BA_4_ORF1a_Del_141143_PMMoV", variantColors.get("BA_4_ORF1a_Del_141143_PMMoV"), "circle", singlePlant)}

${plotvariant("HV_6970_Del_PMMoV", variantColors.get("HV_6970_Del_PMMoV"), "circle", singlePlant)}

${plotvariant("BA_2_75_S_147E_S_152R_PMMoV", variantColors.get("BA_2_75_S_147E_S_152R_PMMoV"), "circle", singlePlant)}

${plotvariant("XBB_bkpt_PMMoV", variantColors.get("XBB_bkpt_PMMoV"), "circle", singlePlant)}

` 35:T4de,For each plant below, we have on the left the values for ${textcolor('all variants (N) / PMMoV', "black")}; ${textcolor(variantNames.get("Delta_156157_PMMoV"), variantColors.get("Delta_156157_PMMoV"))}; ${textcolor(variantNames.get("Del_143145_PMMoV"), variantColors.get("Del_143145_PMMoV"))}; ${textcolor(variantNames.get("BA_2_LPPA24S_PMMoV"), variantColors.get("BA_2_LPPA24S_PMMoV"))}; ${textcolor(variantNames.get("BA_4_ORF1a_Del_141143_PMMoV"), variantColors.get("BA_4_ORF1a_Del_141143_PMMoV"))}; ${textcolor(variantNames.get("HV_6970_Del_PMMoV"), variantColors.get("HV_6970_Del_PMMoV"))}; ${textcolor(variantNames.get("BA_2_75_S_147E_S_152R_PMMoV"), variantColors.get("BA_2_75_S_147E_S_152R_PMMoV"))}; ${textcolor(variantNames.get("XBB_bkpt_PMMoV"), variantColors.get("XBB_bkpt_PMMoV"))}; On the right, we have ratio of each variant to the total covid (for all variants) found in the wastewater. This way we can see both what the values were and the ratios. *Because samples are imperfect, there are times that the variant's value can exceed (be greater than) the value for all variants, especially during the period where there was less covid RNA circulating overall (in autumn 2021, for example). *36:Tac2,variantPercentPlot = function(variant, smooth = false, facet = false, showLines = "none", showPoints = "for all"){ let variantMetric = smooth ? variant + smoothing : variant; let metric = smooth ? variant + "_N_Gene" + smoothing : variant + "_N_Gene" let plotObj = { marks: [ Plot.frame({strokeWidth: 2, stroke: variantColors.get(variant)}), Plot.ruleY([1], {strokeDasharray: "2,2"}), showLines == "for all" ? Plot.line(deltaDataFiltered, { filter: d => !plantstohighlight.includes(d.Plant), x: "date", y: d => d[metric], stroke: facet ? "#555" : "#aaa", z: "Plant", strokeOpacity: facet ? .9 : .5, }) : null, ["for all", "for highlighted locations only"].includes(showLines) ? Plot.line(deltaDataFiltered, { filter: d => plantstohighlight.includes(d.Plant), x: "date", y: d => d[metric], r: 5, stroke: d => plantColors.get(d.Plant), strokeOpacity: .9, z: "Plant", sort: d => d.date }) : null, showPoints == "for all" ? Plot.dot(deltaDataFiltered, { filter: d => !plantstohighlight.includes(d.Plant), x: "date", y: d => d[metric], r: 3, fill: facet ? "#555" : "#aaa", fillOpacity: facet ? .9 : .5, symbol: d => d[metric] < ymax ? "circle" : "triangle", title: d => d.Plant + "\n" + d.dateformatted + "\n" + variantMetric + " / N gene: " + d3.format(".0%")(d[metric]) }) : null, ["for all", "for highlighted locations only"].includes(showPoints) ? Plot.dot(deltaDataFiltered, { filter: d => plantstohighlight.includes(d.Plant), x: "date", y: d => d[metric], r: 5, fill: d => plantColors.get(d.Plant), fillOpacity: .9, stroke: "black", strokeWidth: 1, symbol: d => d[metric] < ymax ? "circle" : "triangle", title: d => d.Plant + "\n" + d.dateformatted + "\n" + variant + " / N gene: " + d3.format(".0%")(d[metric]) }) : null ], y: { tickFormat: d3.format(".0%"), domain: [0, ymax], clamp: true, label: variantNames.get(variant) + " / N Gene" + (smoothPoints ? " (5-day trimmed mean)" : "") }, x: { label: "date of sample taken →" }, width: chartWidth, height: chartWidth * .5, }; if(facet){ plotObj.facet = { data: deltaDataFiltered, y: "Plant", label: null, marginRight: 24 }; plotObj.fy = { padding: .2, tickRotate: 90, }; plotObj.marginRight = 20; plotObj.width = Math.min(width / 2.2, 600); plotObj.height = plantstoshow.length * 220; }; return Plot.plot(plotObj) }37:[] 2f:{"id":"53c00d99947732fb","slug":"scan-location-compare-variants","title":"SCAN: Location Compare for Variants","thumbnail":"b848fc6ee7186271538911b10e3c774dc2175b1bca8c23293116c3d97c39904c","access_level":"public","create_time":"$D2022-01-21T04:02:23.679Z","update_time":"$D2023-01-30T17:46:32.759Z","view_time":null,"first_public_time":"$D2022-06-29T19:54:08.639Z","fork":false,"stars":1,"starred":false,"owner":{"type":"team","id":"f5c920385539a3ff","login":"zanarmstrong","name":"Zan","avatar_url":"https://avatars-next.observableusercontent.com/6e7b2ebb871b8823e6704e8c9e5c1c99715a93c9affacad83335afe2fed062a4","tier":"starter_2024"},"version":1118,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"440a5f5ea2b8acfa","login":"zanarmstrong","name":"Zan","avatar_url":"https://avatars-next.observableusercontent.com/6e7b2ebb871b8823e6704e8c9e5c1c99715a93c9affacad83335afe2fed062a4","tier":null}],"members":[{"type":"individual","id":"440a5f5ea2b8acfa","login":"zanarmstrong","name":"Zan","avatar_url":"https://avatars-next.observableusercontent.com/6e7b2ebb871b8823e6704e8c9e5c1c99715a93c9affacad83335afe2fed062a4","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"subscribed":null,"forks":1,"collection":{"id":"684c25422f321f10","slug":"covid-scan","title":"SCAN","owner":{"id":"f5c920385539a3ff","login":"zanarmstrong","name":"Zan"}},"type":"notebook","body":{"title":"SCAN: Location Compare for Variants","cells":[{"id":0,"value":"# SCAN: Location Compare for Variants\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":541,"value":"$31","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"intro","database":"$undefined"},{"id":73,"value":"viewof plantstoshow = Inputs.checkbox(Plants, {label: \"Locations to show: \", value: Plants})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":428,"value":"*In the charts below, any plants selected here will be \"highlighted\" to draw more attention to these plants while the rest of the locations selected in \"locations to show\" will be shown in grey. So, for example, if you want to compare Oceanside to San Jose and Palo Alto you might select all three in \"locations to show\" but just highlight Oceanside. *","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"selectionDescription","database":"$undefined"},{"id":78,"value":"viewof plantstohighlight = Inputs.checkbox(Plants, {label: \"Locations to highlight: \", value: []})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"viewof num_weeks = Inputs.range([2, d3.timeWeek.count(new Date(\"2020-11-01\"), new Date())], {label: \"Number of weeks to show (prior to today)\", value: 52, step: 1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":338,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":787,"value":"minWidth = 400","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":793,"value":"chartWidth = width / 2.1 < minWidth ? width : width / 2.1","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":511,"value":"*Note: the triangles along the top of the chart represent values that are greater than the max of the y-axis.*","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"notetriangles","database":"$undefined"},{"id":149,"value":"viewof ymax = Inputs.range([1,2.5], {label: \"y-max\", value: 1.1, step: .1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":747,"value":"*Use the radio buttons to choose to use 5-day trimmed smoothing for the points, to add a smoothed line for the highlighted locations or all locations, or to hide some / all of the points. *","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"smoothinginstructions","database":"$undefined"},{"id":579,"value":"viewof smoothPoints = Inputs.radio(new Map([[\"each point showing 5-day trimmed value\", true], [\"each point showing just that day's data\", false]]), {label: \"Select to smooth / not smooth the data\", value: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":641,"value":"viewof showLines = Inputs.radio([\"for all\", \"for highlighted locations only\", \"none\"], \n {label: \"Show smoothed (5-day trimmed mean) lines: \", value: \"none\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":653,"value":"viewof showPoints = Inputs.radio([\"for all\", \"for highlighted locations only\", \"none\"], \n {label: \"Show points: \", value: \"for all\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":330,"value":"----","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"breaker1","database":"$undefined"},{"id":716,"value":"### Per location (plant) charts for Delta and Omicron","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"perlocationheader","database":"$undefined"},{"id":674,"value":"In the following charts, each row is a single location (showing the same ratio metrics as above).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"perlocationdesc","database":"$undefined"},{"id":731,"value":"*Note: The values for the points are ${smoothPoints ? \"**not\" : \"**\"} smoothed** with a 5-day trimmed mean, based on the radio button above. *","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"perlocationsmoothednote","database":"$undefined"},{"id":723,"value":"viewof showLinesFaceted = Inputs.radio([\"for all\", \"for highlighted locations only\", \"none\"], \n {label: \"Show smoothed (5-day trimmed mean) lines: \", value: \"none\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":727,"value":"viewof showPointsFaceted = Inputs.radio([\"for all\", \"for highlighted locations only\", \"none\"], \n {label: \"Show points: \", value: \"for all\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":384,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1042,"value":"variantsToShow","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":762,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"break2","database":"$undefined"},{"id":752,"value":"### Focus on a single location","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"singlelocheader","database":"$undefined"},{"id":399,"value":"Let's just look at delta vs all variants and omicron vs all variants for just one location (plant) at a time. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"descA","database":"$undefined"},{"id":404,"value":"viewof singlePlant = Inputs.select(Plants, {label: \"Select plant to focus on: \", value: \"Oceanside\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"viewof ymaxValues = Inputs.range([0, .0040], {label: \"ymax for charts below\", value: .001})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":230,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":311,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"break3","database":"$undefined"},{"id":766,"value":"### Values and ratios charts side-by-side","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"headersidebyside","database":"$undefined"},{"id":411,"value":"$35","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"descsidebysidefaceted","database":"$undefined"},{"id":506,"value":"boundplantstoshow = Inputs.bind(Inputs.checkbox(Plants, {label: \"Locations to show: \", value: Plants}), viewof plantstoshow)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":274,"value":"sidebysidevalueandratio = html`

${textcolor('All SARS-CoV-2 (N gene)', \"black\")} compared to each variant

Ratio of each variant to all SARS-CoV-2 (N gene)

${valuePlot()}

${asAPercentOfN()}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":537,"value":"Charts built in [Observable](https://observablehq.com/), with [Observable Plot](https://observablehq.com/@observablehq/plot). ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"obscredit","database":"$undefined"},{"id":775,"value":"----","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":322,"value":"### Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":599,"value":"deltaDataFiltered","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":326,"value":"$36","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":342,"value":"variantColors","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":247,"value":"valuePlot = function(){\n\n \n return Plot.plot({\n marks: [\n Plot.frame({stroke: \"#eee\"}),\n Plot.dot(deltaDataFiltered, {\n x: \"date\",\n y: d => d.N_PMMoV,\n r: 2,\n fill: \"#444\"\n })].concat(\n variantsToShow.map(\n variant => {\n return Plot.dot(deltaDataFiltered, {\n x: \"date\",\n y: d => d[variant + \"_PMMoV\"],\n symbol: \"circle\",\n fill: variantColors.get(variant + \"_PMMoV\")\n })\n })\n ),\n facet: {\n data: deltaDataFiltered,\n y: \"Plant\",\n marginRight: 100,\n },\n fy: {\n padding: .2\n },\n y: {\n domain: [0, ymaxValues],\n clamp: true\n },\n marginLeft: 60,\n height: plantstoshow.length * 220,\n width: width / 2.05\n})\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":253,"value":"asAPercentOfN = function(){\n return Plot.plot({\n marks: [\n Plot.frame({stroke: \"#eee\"}),\n Plot.ruleY([1], {strokeDasharray: \"2,2\"})\n ].concat(\n variantsToShow.map(\n variant => {\n return Plot.dot(deltaDataFiltered, {\n x: \"date\",\n y: d => d[variant + \"_PMMoV\"] / d.N_PMMoV,\n r: d => plantstohighlight.includes(d.Plant),\n fill: variantColors.get(variant + \"_PMMoV\"),\n strokeWidth: 1,\n symbol: d => d[variant + \"_PMMoV\"] / d.N_PMMoV < ymax ? \"circle\" : \"triangle\"\n })\n })\n ),\n y: {\n tickFormat: d3.format(\".0%\"),\n domain: [0, ymax],\n clamp: true\n },\n r: {\n domain: [true, false],\n range: [4,3]\n },\n facet: {\n data: deltaDataFiltered,\n y: \"Plant\",\n marginRight: 100,\n },\n \n fy: {\n padding: .2\n },\n marginLeft: 60,\n height: plantstoshow.length * 220,\n width: width / 2.05\n})\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":189,"value":"plotvariant = function(variant, color, symbol, plant){\n const data = deltaData.filter(d => plant == d.Plant)\n return Plot.plot({\n marks: [\n Plot.frame({stroke: \"#eee\"}),\n Plot.dot(data, {\n x: \"date\",\n y: d => d.N_PMMoV,\n fill: \"#444\"\n }),\n Plot.dot(data, {\n x: \"date\",\n y: d => d[variant],\n //symbol: symbol,\n fill: color\n }),\n ],\n facet: {\n data: data,\n y: \"Plant\",\n label: null\n },\n fy:{\n tickRotate: 90 \n },\n y: {\n domain: [0, ymaxValues],\n clamp: true,\n },\n marginLeft: 60,\n height: 220,\n width: Math.min(width, 700)\n})\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"parseData = (d) => {\n d.datetime = d.Date.replace(' ', 'T')\n if (new Date(d.datetime) >= new Date(earliestDate)) { \n let r = {\n date: timeParse(d.datetime.substring(0, 10)),\n dateformatted: d.datetime.substring(0, 10)\n };\n metrics.forEach((metric) => (r[metric + smoothing] = +d[metric + smoothing]));\n metrics.forEach((metric) => (r[metric] = +d[metric]));\n r[\"Plant\"] = d.Plant;\n return r;\n }\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"earliestDate = timeFormat(earliestDateUnformatted)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"earliestDateUnformatted = d3.timeDay.offset(new Date(), -(7 * num_weeks))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"smoothing = \"_trimmed5\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"metrics = variantsToShow.reduce(\n (p, c) => p.concat([c + '_PMMoV', c + '_N_Gene', c + '_gc_g_dry_weight']), \n [\"N_PMMoV\"]\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"deltaData = d3.csv(url, parseData)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1117,"value":"deltaDataFiltered[3032]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":86,"value":"deltaDataFiltered = deltaData.filter(d => plantstoshow.includes(d.Plant))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"d3.csv(url)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":109,"value":"plantColors = new Map(Plants.map((d,i) => [d, colors[i]]))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":103,"value":"colors = [\"#5b859e\",\"#1e395f\",\"#75884b\",\"#1e5a46\",\"#df8d71\",\"#af4f2f\",\"#d48f90\",\"#732f30\",\"#ab84a5\",\"#59385c\",\"#d8b847\",\"#b38711\"]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":279,"value":"variantColors = new Map(\n variantsToShowAndNormalized.map(ob => {\n return [ob, metricsMeta[ob].color]\n })\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":811,"value":"variantNames = new Map(\n variantsToShowAndNormalized.map(ob => {\n return [ob, metricsMeta[ob].label]\n })\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":999,"value":"variantsToShowAndNormalized = \nvariantsToShow.concat(variantsToShow.map(a => a + \"_PMMoV\"))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":978,"value":"variantsToShow = [\n \"Delta_156157\",\n \"Del_143145\",\n \"BA_2_LPPA24S\",\n \"BA_4_ORF1a_Del_141143\",\n \"HV_6970_Del\",\n \"BA_2_75_S_147E_S_152R\",\n \"XBB_bkpt\", // XBB\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":68,"value":"Plants = [...new Set([\"Palo Alto\", \"San Jose\", \"Sunnyvale\",\"Gilroy\", \"Silicon Valley\", \"Sacramento\", \"Oceanside\", \"CODIGA\", \"Southeast San Francisco\"])]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3,"value":"import { url, cutoffDates, timeFormat, timeParse, metricsMeta } from \"6c55536820c54786\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":265,"value":"import {textcolor} from \"@observablehq/text-color-annotations-in-markdown\"\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":451,"value":"import {addTooltips} from \"@mkfreeman/plot-tooltip\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"todo: check date handling","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W37","stdlib":"1","titling":"auto"}} 30:"$2f:body"