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feat: add "others" as a variant #342

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feat: add "others" as a variant #342

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16 changes: 14 additions & 2 deletions scripts/clusters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1030,7 +1030,7 @@
},

"22D": { #BA.2.75
"snps": [3927, 26275, 3796], #TGT = C3927T, A26275G, C3796T
"snps": [3927, 26275, 3796], #TGT = C3927T, A26275G, C3796T
"snps_with_base": ["3927T", "26275G", "3796T"],
"cluster_data": [],
"nextstrain_build": True,
Expand Down Expand Up @@ -1362,7 +1362,7 @@
},
},

# C.37
# C.37
"21GLambda": {
"snps": [7424, 23031, 24138], # ORF1a 2387 (7424G) #S 490 (23031C) 859 (24138A)
"snps_with_base": ["7424G", "23031C", "24138A"],
Expand Down Expand Up @@ -2509,4 +2509,16 @@
# "ORFTEN30": {'snps': [29644], 'exclude_snps': [22226], 'cluster_data': [], "build_name": "ORF10.V30", "display_name": "ORF10:V30"}
# "N220re": {'snps': [28931,29644], 'exclude_snps': [22226], 'cluster_data': [], "build_name": "N.A220Vre", "display_name": "N:A220Vre"}
# "B1139" {'snps': [28486,28867], 'exclude_snps': [], 'cluster_data': [], "build_name": "B1139", "display_name": "B1139"}

"others": {
"build_name": "others",
"cluster_data": [],
"col": "#222222",
"snps": [],
"display_name": "others",
"graphing": False,
"important": False,
"nextstrain_build": False,
"type": "variant"
}
Comment on lines +2513 to +2523
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@ivan-aksamentov ivan-aksamentov Aug 9, 2022 •
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This is the definition of the "others" variant in clusters.py. This object will be emitted into clusters.json along with other variants.

It should be the last object in the list to keep the display order of area segments on the plot the same. However you can play with the order to your liking.

}
14 changes: 13 additions & 1 deletion web/data/clusters.json
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Expand Up @@ -8592,6 +8592,18 @@
23277
],
"type": "do_not_display"
},
{
"build_name": "others",
"cluster_data": [],
"snps": [],
"col": "#222222",
"country_info": [],
"display_name": "others",
"graphing": false,
"important": false,
"nextstrain_build": false,
"type": "variant"
}
]
}
}
3 changes: 2 additions & 1 deletion web/data/perCountryDataCaseCounts.json
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Expand Up @@ -30,7 +30,8 @@
"22C (Omicron)",
"22D (Omicron)",
"S:677H.Robin1",
"S:677P.Pelican"
"S:677P.Pelican",
"others"
],
Comment on lines +33 to 35
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@ivan-aksamentov ivan-aksamentov Aug 9, 2022 •
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"others" needs to be added into the list of cluster_names in json data. Here I illustrate what the result should look like for cases data. This is a manual addition and is not enforced in code. Python scripts will need to be changed for that (for cases and other plots if applicable).

"distributions": [
{
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12 changes: 1 addition & 11 deletions web/src/components/Cases/CasesPlot.tsx
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Expand Up @@ -8,7 +8,7 @@ import ReactResizeDetector from 'react-resize-detector'

import type { PerCountryCasesDistributionDatum } from 'src/io/getPerCountryCasesData'
import { ticks, timeDomain } from 'src/io/getParams'
import { CLUSTER_NAME_OTHERS, getClusterColor } from 'src/io/getClusters'
import { getClusterColor } from 'src/io/getClusters'
import { formatDateHumanely } from 'src/helpers/format'
import { adjustTicks } from 'src/helpers/adjustTicks'
import { PlotPlaceholder } from 'src/components/Common/PlotPlaceholder'
Expand Down Expand Up @@ -90,16 +90,6 @@ export function CasesPlotComponent({ cluster_names, distribution }: CasesPlotPro
/>
))}

<Area
type="monotone"
dataKey={CLUSTER_NAME_OTHERS}
stackId="1"
stroke="none"
fill={theme.clusters.color.others}
fillOpacity={1}
isAnimationActive={false}
/>

<CartesianGrid stroke={theme.plot.cartesianGrid.stroke} />
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Here I remove the additional ad-hoc area segment from the cases plot. The same should be done for the other plot(s), when they get their own "others" data.


<Tooltip
Expand Down