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Feature/aggregate ffpe tissue in catalogue and chart #68

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merged 6 commits into from
Mar 20, 2024
Merged

Feature/aggregate ffpe tissue in catalogue and chart #68

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251d7e2
feat(chart): add accumulated values property WIP
MatsJohansen87 Mar 18, 2024
0efd88c
feat(chart): add support for accumulated values
MatsJohansen87 Mar 18, 2024
06d6322
feat(catalogue): aggregate frozen and ffpe sample types
MatsJohansen87 Mar 19, 2024
8601bb6
feat(charts): move accumulations input to options
MatsJohansen87 Mar 20, 2024
9dec16d
chore(logs): remove unnecessary console logs
MatsJohansen87 Mar 20, 2024
40214f6
fix(ccp options): divide frozen and ffpe in accumulations
MatsJohansen87 Mar 20, 2024
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34 changes: 33 additions & 1 deletion packages/demo/public/catalogues/catalogue-dktk.json
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Original file line number Diff line number Diff line change
Expand Up @@ -20181,14 +20181,46 @@
{
"value": "histology",
"name": "tumor-tissue-ffpe"
},
{
"value": "sample_kind",
"name": "tissue-ffpe"
},
{
"value": "sample_kind",
"name": "normal-tissue-ffpe"
},
{
"value": "sample_kind",
"name": "other-tissue-ffpe"
}
]
]
},
{
"key": "tumor-tissue-frozen",
"name": "Gewebe schockgefroren",
"description": "Tumorgewebe (Kryo/Frisch)"
"description": "Tumorgewebe (Kryo/Frisch)",
"aggregatedValue": [
[
{
"value": "sample_kind",
"name": "tissue-frozen"
},
{
"value": "sample_kind",
"name": "tumor-tissue-frozen"
},
{
"value": "sample_kind",
"name": "normal-tissue-frozen"
},
{
"value": "sample_kind",
"name": "other-tissue-frozen"
}
]
]
},
{
"key": "tissue-other",
Expand Down
28 changes: 24 additions & 4 deletions packages/demo/public/options.json
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Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,29 @@
"hintText": [
"Verteilung der Probentypen die mit den identifizierten Patienten verbunden sind."
],
"accumulatedValues": [
{
"name": "ffpe-tissue",
"values": [
"tissue-ffpe",
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"tumor-tissue-ffpe",
"normal-tissue-ffpe",
"other-tissue-ffpe"
]
},
{
"name": "frozen-tissue",
"values": [
"tissue-frozen",
"tumor-tissue-frozen",
"normal-tissue-frozen",
"other-tissue-frozen"
]
}
],
"tooltips": {
"tissue-ffpe": "Gewebe FFPE",
"tissue-frozen": "Gewebe schockgefroren",
"ffpe-tissue": "Gewebe FFPE",
"frozen-tissue": "Gewebe schockgefroren",
"tissue-other": "Gewebe, Andere Konservierungsart",
"whole-blood": "Vollblut",
"blood-serum": "Serum",
Expand All @@ -106,8 +126,8 @@
"derivative-other": "Derivat, Andere"
},
"legendMapping":{
"tissue-ffpe": "Gewebe FFPE",
"tissue-frozen": "Gewebe schockgefroren",
"ffpe-tissue": "Gewebe FFPE",
"frozen-tissue": "Gewebe schockgefroren",
"tissue-other": "Gewebe, Andere Konservierungsart",
"whole-blood": "Vollblut",
"blood-serum": "Serum",
Expand Down
54 changes: 52 additions & 2 deletions packages/lib/src/components/results/ChartComponent.wc.svelte
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,6 @@
export let filterRegex: string = "";
export let groupingLabel: string = "";
export let viewScales: boolean = chartType !== "pie" ? true : false;

let options: ChartOption;
$: options =
($lensOptions?.chartOptions &&
Expand Down Expand Up @@ -171,6 +170,23 @@
},
};

const accumulateValues = (
responseStore: ResponseStore,
valuesToAccumulate: string[],
catalogueGroupCode: string,
): number => {
let aggregatedData = 0;

valuesToAccumulate.forEach((value: string) => {
aggregatedData += getAggregatedPopulationForStratumCode(
responseStore,
value,
catalogueGroupCode,
);
});
return aggregatedData;
};

/**
* gets the aggregated population for a given stratum code
* @param responseStore - the response store
Expand Down Expand Up @@ -242,6 +258,36 @@
});
}

/**
* if accumulated values are set, accumulate the values of the given stratum codes and adds them to the chart
* e.g. {name: "frozen-tissue", values: ["tissue-frozen","tissue-ffpe"]}
* will remove the values from the chart and add their accumulated value to "frozen-tissue"
*/
if (
options.accumulatedValues !== undefined &&
options.accumulatedValues.length > 0
) {
options.accumulatedValues.forEach((valueToAccumulate) => {
const aggregationCount: number = accumulateValues(
responseStore,
valueToAccumulate.values,
catalogueGroupCode,
);

combinedSubGroupData.data.push(aggregationCount);
combinedSubGroupData.labels.push(valueToAccumulate.name);

for (let i = 0; i < combinedSubGroupData.labels.length; i++) {
const element: string = combinedSubGroupData.labels[i];
if (valueToAccumulate.values.includes(element)) {
combinedSubGroupData.labels.splice(i, 1);
combinedSubGroupData.data.splice(i, 1);
i--;
}
}
});
}

return {
labels: combinedSubGroupData.labels,
data: [
Expand Down Expand Up @@ -384,7 +430,11 @@
* will be aggregated in groups if a divider is set
* eg. 'C30', 'C31.1', 'C31.2' -> 'C31' when divider is '.'
*/
let chartData = getChartDataSets(responseStore, chartLabels);
let chartData: ChartDataSets = getChartDataSets(
responseStore,
chartLabels,
);

chart.data.datasets = chartData.data;
chartLabels = chartData.labels;

Expand Down
1 change: 0 additions & 1 deletion packages/lib/src/stores/query.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,6 @@ export const addStratifier = ({
groupRange,
}): void => {
let queryItem: QueryItem;
console.log(catalogue);
catalogue.forEach((parentCategory: Category) => {
if ("childCategories" in parentCategory) {
parentCategory.childCategories.forEach(
Expand Down
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