30:[] 2e:{"title":"Embeds for CODIGA","cells":[{"id":0,"value":"md`# Embeds for CODIGA`","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"howto = html`\n

How to read the plots?

1. Solid trend lines show the quantity of RNA from 2 SARS-COV-2 genes, N and S. \n

2. The line for BA.2 signifies the quantity from *only* Omicron variants BA.2, BA.4, and BA.5 (specifically tracking variant defined by \"LPPA24S\"). The line for BA.4 signifies the quantity from *only* Omicron variant BA.4 (specifically tracking variants defined by \"ORF1a_Del_141143\").

3. All values are normalized by PMMoV to account for “fecal strength”.

4. Higher value on Y axis indicates more SARS-COV-2 virus. Values shown represent a trimmed 5-day moving average.

5. Dashed horizontal line provides a comparison to 2 weeks ago

6. Black marks on x-axis indicate that the data was sampled that day (typically daily, but sometimes a day is missed)

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":22,"value":"creditLink = credit","pinned":false,"hidden":false,"mode":"ojs"},{"id":201,"value":"defaultTimeFrame = \"Last 12 weeks\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":97,"value":"viewof selectedTimeFrame = Inputs.select(Object.keys(timeframes), {label: \"Timeframe: \", value: defaultTimeFrame})","pinned":false,"hidden":false,"mode":"ojs"},{"id":321,"value":"viewof metrics = Inputs.checkbox(metricsAvailable, {\n label: \"metrics\",\n value: [\"N_PMMoV\",\"HV_6970_Del_PMMoV\", \"XBB_bkpt_PMMoV\"],\n format: d => metricsMeta[d].label\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":6,"value":"codiga = plotOverview('CODIGA', {cutoffdate: '2023-01-02'})","pinned":false,"hidden":false,"mode":"ojs"},{"id":70,"value":"md`## Change these to adjust aspect ratio\n\nValues are in pixels. This is of the entire SVG for each chart, not just the inside of the chart.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":54,"value":"totalwidth = Math.min(Math.max(width, 400), 1200)","pinned":true,"hidden":false,"mode":"ojs"},{"id":53,"value":"totalheight = Math.min(Math.max(totalwidth / 2, 300), 400)","pinned":true,"hidden":false,"mode":"ojs"},{"id":83,"value":"md`### Change num_weeks to change the number of weeks of data to show`","pinned":false,"hidden":false,"mode":"ojs"},{"id":77,"value":"num_weeks = timeframes[selectedTimeFrame]","pinned":false,"hidden":false,"mode":"ojs"},{"id":39,"value":"md`### Change these to change the labels on the charts`","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"xlabel = \"Date of Sample\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":12,"value":"ylabel = \"Quantity of RNA, normalized\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":47,"value":"md`## Don't change this`","pinned":false,"hidden":false,"mode":"ojs"},{"id":118,"value":"timeframes = ({'Last 4 weeks': 4,\n 'Last 6 weeks': 6,\n 'Last 12 weeks': 12,\n 'Since Dec 3, 2021 (start of tracking Omicron)': weeksSince(\"2021-12-03\"),\n 'Since July 29, 2021 (beginning of tracking)': weeksSince(\"2021-07-29\")\n })","pinned":true,"hidden":false,"mode":"ojs"},{"id":115,"value":"weeksSince = function(datestring){\n return (d3.timeDay.count(d3.timeParse(\"%Y-%m-%d\")(datestring), new Date()) - 1) / 7\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":205,"value":"mainTitle = \"SARS-CoV-2 genes (N, S), and variant-specific (ie. BA.4+BA.5 Omicron)\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":227,"value":"metricsAvailable = [\"N_PMMoV\",\"S_PMMoV\",\"Del_143145_PMMoV\", \"BA_2_LPPA24S_PMMoV\", \"BA_4_ORF1a_Del_141143_PMMoV\",\"HV_6970_Del_PMMoV\", \"BA_2_75_S_147E_S_152R_PMMoV\", \"XBB_bkpt_PMMoV\", ]\n","pinned":true,"hidden":false,"mode":"ojs"},{"id":226,"value":"codigaOnly = rawdata.filter(d => d.Plant == \"CODIGA\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":244,"value":"[...new Set(rawdata.map(d => d.Plant))]","pinned":true,"hidden":false,"mode":"ojs"},{"id":225,"value":"rawdata","pinned":true,"hidden":false,"mode":"ojs"},{"id":2,"value":"import {d3, plotOverview, credit, rawdata, metricsMeta} with {xlabel, ylabel, totalheight, totalwidth, num_weeks, mainTitle, metrics} from \"6c55536820c54786\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":233,"value":"# Exploratory Analysis: compare N / S ratio. ","pinned":false,"hidden":false,"mode":"md"}],"files":"$W30","stdlib":"1","titling":"auto"}