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Clean Up MetaSUB Dashboard #27

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Clean Up MetaSUB Dashboard #27

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130 changes: 66 additions & 64 deletions src/contrib/metasub/components/samplesunburst.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -9,71 +9,73 @@ interface SampleSunburstPanelProps {
onClickAction: (taxonName: string) => void;
}


const SampleSunburstPanel = (props: SampleSunburstPanelProps) => {
const url =
'/contrib/metasub/sample_sunburst/' +
props.sampleUUID +
'?format=json&min_abundance=0.005';
const [{ data, loading, error }] = usePangeaAxios<SunburstTaxa>({
url: url,
method: 'GET',
});
if (loading) {
return (
<>
<Row>
<h1>Loading...</h1>
<h2>Sample Taxa</h2>
</Row>
</>
);
}
if (error) {
return (
<>
<Row>
<h1>Error</h1>
<h2>Sample Taxa</h2>
<p>{error}</p>
</Row>
</>
);
}
const plotData: Partial<Plotly.PlotData>[] = [
{
type: 'sunburst',
labels: data.taxa,
parents: data.parents,
values: data.abundances,
outsidetextfont: { size: 20, color: '#377eb8' },
leaf: { opacity: 0.4 },
marker: { line: { width: 2 } },
},
];
const layout = {
margin: { l: 0, r: 0, b: 0, t: 0 },
width: 350,
height: 350,
};
return (
<>
<Plot
data={plotData}
layout={layout}
onClick={e =>
props.onClickAction(
e.points[0]?.value
? e.points[0]?.label
? e.points[0]?.label
: ''
: '',
)
}
/>
<h5>Click a sample on the map to see it here.</h5>
<h5>Click a species here to see it on the map.</h5>
</>
);
// const url =
// '/contrib/metasub/sample_sunburst/' +
// props.sampleUUID +
// '?format=json&min_abundance=0.005';
// const [{ data, loading, error }] = usePangeaAxios<SunburstTaxa>({
// url: url,
// method: 'GET',
// });
// if (loading) {
// return (
// <>
// <Row>
// <h1>Loading...</h1>
// <h2>Sample Taxa</h2>
// </Row>
// </>
// );
// }
// if (error) {
// return (
// <>
// <Row>
// <h1>Error</h1>
// <h2>Sample Taxa</h2>
// <p>{error}</p>
// </Row>
// </>
// );
// }
// const plotData: Partial<Plotly.PlotData>[] = [
// {
// type: 'sunburst',
// labels: data.taxa,
// parents: data.parents,
// values: data.abundances,
// outsidetextfont: { size: 20, color: '#377eb8' },
// leaf: { opacity: 0.4 },
// marker: { line: { width: 2 } },
// },
// ];
// const layout = {
// margin: { l: 0, r: 0, b: 0, t: 0 },
// width: 350,
// height: 350,
// };
// return (
// <>
// <Plot
// data={plotData}
// layout={layout}
// onClick={e =>
// props.onClickAction(
// e.points[0]?.value
// ? e.points[0]?.label
// ? e.points[0]?.label
// : ''
// : '',
// )
// }
// />
// <h5>Click a sample on the map to see it here.</h5>
// <h5>Click a species here to see it on the map.</h5>
// </>
// );
return (<></>)
};

export default SampleSunburstPanel;
91 changes: 46 additions & 45 deletions src/contrib/metasub/components/taxonabundancepanel.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -17,56 +17,57 @@ const generateUrl = (taxonName: string): string => {
};

const TaxaAbundancePanel = (props: TaxaAbundancePanelProps) => {
const [{ data, loading, error }, refetch] = usePangeaAxios<{
[key: string]: CitiesTaxonResult;
}>({ url: '', method: 'GET' }, { manual: true });
// const [{ data, loading, error }, refetch] = usePangeaAxios<{
// [key: string]: CitiesTaxonResult;
// }>({ url: '', method: 'GET' }, { manual: true });

React.useEffect(() => {
refetch({ url: generateUrl(props.taxonName) });
}, [props.taxonName]);
// React.useEffect(() => {
// refetch({ url: generateUrl(props.taxonName) });
// }, [props.taxonName]);

const currentData = ((data || {}).results || {})[props.taxonName];
// const currentData = ((data || {}).results || {})[props.taxonName];

if (loading || currentData === undefined) {
return (
<>
<Row>
<h1>Loading...</h1>
<h2>Taxon Abundance</h2>
</Row>
</>
);
}
// if (loading || currentData === undefined) {
// return (
// <>
// <Row>
// <h1>Loading...</h1>
// <h2>Taxon Abundance</h2>
// </Row>
// </>
// );
// }

if (error) {
return (
<>
<Row>
<h1>Error</h1>
<h2> MetaSUB Map</h2>
<p>{error}</p>
</Row>
</>
);
}
// if (error) {
// return (
// <>
// <Row>
// <h1>Error</h1>
// <h2> MetaSUB Map</h2>
// <p>{error}</p>
// </Row>
// </>
// );
// }

const cityAbundances: { [key: string]: CityTaxonAbundance } = currentData; //['results'][props.taxonName];
const plotData: Partial<Plotly.PlotData>[] = Object.keys(cityAbundances).map(
function(cityName: string): Partial<Plotly.PlotData> {
return {
y: cityAbundances[cityName].all_relative_abundances,
type: 'box',
name: cityAbundances[cityName].city_name,
};
},
);
const layout = {
title: '<i>' + props.taxonName + '</i> Abundance in Cities',
margin: { l: 20, r: 0, b: 0, t: 30 },
width: 700,
height: 400,
};
return <Plot data={plotData} layout={layout} />;
// const cityAbundances: { [key: string]: CityTaxonAbundance } = currentData; //['results'][props.taxonName];
// const plotData: Partial<Plotly.PlotData>[] = Object.keys(cityAbundances).map(
// function(cityName: string): Partial<Plotly.PlotData> {
// return {
// y: cityAbundances[cityName].all_relative_abundances,
// type: 'box',
// name: cityAbundances[cityName].city_name,
// };
// },
// );
// const layout = {
// title: '<i>' + props.taxonName + '</i> Abundance in Cities',
// margin: { l: 20, r: 0, b: 0, t: 30 },
// width: 700,
// height: 400,
// };
// return <Plot data={plotData} layout={layout} />;
return (<></>)
};

export default TaxaAbundancePanel;
105 changes: 53 additions & 52 deletions src/contrib/metasub/components/taxonabundancepanelmaterial.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -17,63 +17,64 @@ const generateUrl = (taxonName: string): string => {
};

const TaxaMaterialAbundancePanel = (props: TaxaMaterialAbundancePanelProps) => {
const [{ data, loading, error }, refetch] = usePangeaAxios<{
[key: string]: SurfacesTaxonResult;
}>({ url: '', method: 'GET' }, { manual: true });
// const [{ data, loading, error }, refetch] = usePangeaAxios<{
// [key: string]: SurfacesTaxonResult;
// }>({ url: '', method: 'GET' }, { manual: true });

React.useEffect(() => {
refetch({ url: generateUrl(props.taxonName) });
}, [props.taxonName]);
// React.useEffect(() => {
// refetch({ url: generateUrl(props.taxonName) });
// }, [props.taxonName]);

const currentData = ((data || {}).results || {})[props.taxonName];
// const currentData = ((data || {}).results || {})[props.taxonName];

if (loading || currentData === undefined) {
return (
<>
<Row>
<h1>Loading...</h1>
<h2>Taxon Abundance</h2>
</Row>
</>
);
}
// if (loading || currentData === undefined) {
// return (
// <>
// <Row>
// <h1>Loading...</h1>
// <h2>Taxon Abundance</h2>
// </Row>
// </>
// );
// }

if (error) {
return (
<>
<Row>
<h1>Error</h1>
<h2>Taxon Abundance</h2>
<p>{error}</p>
</Row>
</>
);
}
// if (error) {
// return (
// <>
// <Row>
// <h1>Error</h1>
// <h2>Taxon Abundance</h2>
// <p>{error}</p>
// </Row>
// </>
// );
// }

const surfaceAbundances: {
[key: string]: SurfaceTaxonAbundance;
} = currentData; //['results'][props.taxonName];
const plotData: Partial<Plotly.PlotData>[] = Object.keys(surfaceAbundances)
.filter(function(surfaceName: string): boolean {
return (
surfaceName.length > 0 &&
surfaceAbundances[surfaceName].all_relative_abundances.length >= 10
);
})
.map(function(surfaceName: string): Partial<Plotly.PlotData> {
return {
y: surfaceAbundances[surfaceName].all_relative_abundances,
type: 'box',
name: surfaceAbundances[surfaceName].material_name,
};
});
const layout = {
title: '<i>' + props.taxonName + '</i> Abundance on Surfaces',
margin: { l: 20, r: 0, b: 0, t: 30 },
width: 700,
height: 400,
};
return <Plot data={plotData} layout={layout} />;
// const surfaceAbundances: {
// [key: string]: SurfaceTaxonAbundance;
// } = currentData; //['results'][props.taxonName];
// const plotData: Partial<Plotly.PlotData>[] = Object.keys(surfaceAbundances)
// .filter(function(surfaceName: string): boolean {
// return (
// surfaceName.length > 0 &&
// surfaceAbundances[surfaceName].all_relative_abundances.length >= 10
// );
// })
// .map(function(surfaceName: string): Partial<Plotly.PlotData> {
// return {
// y: surfaceAbundances[surfaceName].all_relative_abundances,
// type: 'box',
// name: surfaceAbundances[surfaceName].material_name,
// };
// });
// const layout = {
// title: '<i>' + props.taxonName + '</i> Abundance on Surfaces',
// margin: { l: 20, r: 0, b: 0, t: 30 },
// width: 700,
// height: 400,
// };
// return <Plot data={plotData} layout={layout} />;
return (<></>)
};

export default TaxaMaterialAbundancePanel;
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