From 6d3273fd1925cae2502b81d312e6b296813a5579 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 8 Feb 2024 17:54:55 +0100
Subject: [PATCH] Remove some dead code
---
components/content/RefseqDb.vue | 153 ++++-------------------------
components/content/StructureDb.vue | 1 -
2 files changed, 19 insertions(+), 135 deletions(-)
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index cff70486..08ca0836 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -225,15 +225,6 @@ const computedDistriSystemOptions = computed(() => {
},
),
- // Plot.barY(
- // toValNormalizePerAssembly,
- // Plot.groupX({ y: "sum" }, {
- // x: 'system', tip: true,
- // sort: { x: "-y" },
- // }),
-
-
- // ),
],
};
});
@@ -309,7 +300,24 @@ const binPlotOptions = ref({
const binPlotGroup = computed(() => {
return Plot.group(
{
- fill: "count"
+ fill: {
+ label: `Normalize by ${selectedTaxoRank.value} clade`,
+ reduceIndex: function (I, X) {
+ const toValAssemblyPerRank = toValue(assemblyPerRank)
+ if (toValAssemblyPerRank?.size > 0) {
+ const clade = X[I[0]][selectedTaxoRank.value]
+ const system = X[I[0]].type
+ // Get the list of item for this group
+ const itemsPerGroup = d3.rollup(I.map(index => {
+ return X[index]
+ }), D => D.length, d => d.type, d => d.Assembly)
+ const countForClade = toValAssemblyPerRank.get(clade).size
+ const frequency = (itemsPerGroup.get(system).size / countForClade) * 100
+ return frequency
+ }
+ return I.length
+ }
+ }
},
{
x: "type",
@@ -335,96 +343,12 @@ const binPlotDataOptions = computed(() => {
},
marks: [
- Plot.cell(data, Plot.group(
- {
- fill: {
- label: `Normalize by ${selectedTaxoRank.value} clade`,
- reduceIndex: function (I, X) {
- const toValAssemblyPerRank = toValue(assemblyPerRank)
- if (toValAssemblyPerRank?.size > 0) {
- const clade = X[I[0]][selectedTaxoRank.value]
- const system = X[I[0]].type
- console.log(I)
- console.log(X)
- // Get the list of item for this group
- const itemsPerGroup = d3.rollup(I.map(index => {
- return X[index]
- }), D => D.length, d => d.type, d => d.Assembly)
- console.log(itemsPerGroup)
- // console.log(clade)
- // console.log(toValAssemblyPerRank.get(clade))
- const countForClade = toValAssemblyPerRank.get(clade).size
- // console.log(countForClade)
- // console.log(I);
- // console.log(X);
-
- const frequency = (itemsPerGroup.get(system).size / countForClade) * 100
- console.log(frequency)
- return frequency
- }
- return I.length
- }
- }
- },
- {
- x: "type",
- y: selectedTaxoRank.value,
- tip: true,
- inset: 0.5,
- sort: { y: "fill" }
- }))
+ Plot.cell(data, toValue(binPlotGroup))
]
} : null
-
- // const toValNormalizePerAssembly = toValue(normalizePerAssembly)
- // return toValNormalizePerAssembly?.length > 0 ? {
- // ...binPlotOptions.value,
- // width: width.value,
-
- // color: {
- // ...binPlotOptions.value.color,
- // type: scaleType.value,
- // tickFormat: '~s',
- // ticks: scaleType.value === 'symlog' ? 3 : 5,
- // },
- // marks: [
- // Plot.cell(
- // toValNormalizePerAssembly ?? [],
- // Plot.group({
- // fill: "count"
- // }, {
- // x: "system",
- // y: "rank",
- // tip: true,
- // inset: 0.5,
- // sort: { y: "fill" }
- // })),
- // ]
-
- // } : null
-
})
-const systemPerAssemblyPerRank = computed(() => {
- const toValueAllHits = toValue(allHits)
- console.log("all hits dans system per...")
- console.log(toValueAllHits)
- if (toValueAllHits && toValueAllHits?.hits?.length > 0) {
- return d3.rollup(toValueAllHits.hits, D => D.length, d => d[toValue(selectedTaxoRank)], d => d.Assembly, d => d.type)
- }
-})
-
-const systemPerRankPerAssembly = computed(() => {
- const toValueAllHits = toValue(allHits)
- console.log("all hits dans system per...")
- console.log(toValueAllHits)
- if (toValueAllHits && toValueAllHits?.hits?.length > 0) {
- return d3.rollup(toValueAllHits.hits, D => D.length, d => d[toValue(selectedTaxoRank)], d => d.type, d => d.Assembly)
- }
-})
-
-
const assemblyPerRank = computed(() => {
const toValueAllHits = toValue(allHitsDb)
@@ -433,46 +357,7 @@ const assemblyPerRank = computed(() => {
}
})
-const ranks = computed(() => {
- const toValAssemblyPerRank = toValue(assemblyPerRank)
- console.log("dans le ranks computed")
- console.log(toValAssemblyPerRank)
- if (toValAssemblyPerRank && toValAssemblyPerRank?.size > 0) {
- console.log(toValAssemblyPerRank.keys())
-
- return [...toValAssemblyPerRank.keys()]
- }
-})
-
-const normalizePerAssembly = computed(() => {
- const toValRanks = toValue(ranks)
- const toValAssemblyPerRank = toValue(assemblyPerRank)
- const toValSystemPerAssemblyPerRank = toValue(systemPerAssemblyPerRank)
- const normalizedSystemCount = []
-
- console.log("dans computed normalize per assembly")
- console.log(toValRanks)
- console.log(toValAssemblyPerRank)
- console.log(toValSystemPerAssemblyPerRank)
- if (toValRanks && toValAssemblyPerRank && toValSystemPerAssemblyPerRank) {
- for (const rank of toValRanks) {
- // get list assembly for this rank
- console.log(rank)
- const assemblies = [...toValAssemblyPerRank.get(rank).keys()]
- for (const assembly of assemblies) {
- // get list
- const countAssemblyPerRank = toValAssemblyPerRank.get(rank).get(assembly)
- const systems = toValSystemPerAssemblyPerRank.get(rank).get(assembly).keys()
- for (const system of systems) {
- const countSystem = toValSystemPerAssemblyPerRank.get(rank).get(assembly).get(system)
- normalizedSystemCount.push({ rank, assembly, system, frequency: countSystem / countAssemblyPerRank })
- }
- }
- }
- }
- return normalizedSystemCount
-})
const scaleType = ref("linear")
const systemsDistributionPlot = ref<ComponentPublicInstance | null>(null)
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 27e5c74d..10805d56 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -124,7 +124,6 @@ const dataTableServerProps = computed(() => {
function toFolseekUrl(item: Item) {
const url = joinURL("/" + item.System_name_ok, item.Foldseek_name)
const { refinedUrl } = useRefinedUrl(url)
- console.log(toValue(refinedUrl))
return toValue(refinedUrl)
}
--
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