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InteractionWrapper.vue
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InteractionWrapper.vue
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<template>
<v-container fluid>
<v-row>
<v-col cols="3">
<v-card class="ma-1">
<v-tabs
v-model="UiModel.tabIndex"
grow
dense
dark
:background-color="
$store.state.selectedOrganismShown.secondaryColor
"
>
<v-tabs-slider
:color="$store.state.selectedOrganismShown.primaryColor"
></v-tabs-slider>
<v-tab href="#tab-0"> Relations </v-tab>
<v-tab href="#tab-1" :disabled="!UiModel.visibleNode">
Node information
</v-tab>
<v-tab href="#tab-2" :disabled="!UiModel.visibleRetrieval">
Options
</v-tab>
<v-tabs-items v-model="UiModel.tabIndex">
<v-tab-item :value="'tab-0'">
<v-treeview
:items="RelationTypesModel"
item-children="Children"
item-text="Label"
return-object
dense
style="overflow-y: auto; max-height: 500px"
>
<template v-slot:prepend="{ item }">
<v-row>
<div v-html="item.svg"></div>
<v-checkbox
v-if="item.Description"
v-model="item.selected"
:value="item.selected"
:label="item.Name"
dense
class="mt-0 pt-0"
@change="modifiedRelationSelection = true"
></v-checkbox>
</v-row>
</template>
</v-treeview>
<v-col align="middle">
<v-btn
:color="$store.state.selectedOrganismShown.primaryColor"
:loading="loading"
:disabled="loading"
class="ma-2 white--text"
@click="runAnalysis"
>
Run analysis
<v-icon right>fas fa-running</v-icon>
</v-btn>
</v-col>
</v-tab-item>
<v-tab-item :value="'tab-1'">
<v-expansion-panels
multiple
dense
style="overflow-y: auto; max-height: 500px"
class="pa-1"
>
<v-expansion-panel
v-for="(item, i) in NodeModel.nodes"
:key="i"
class="ma-1"
color="secondary"
>
<v-expansion-panel-header>{{
item.Label
}}</v-expansion-panel-header>
<v-expansion-panel-content>
<v-divider />
<v-list dense>
<v-list-item
v-for="(child, j) in item.Children"
:key="j"
>
<v-list-item-title>{{
child.ResourceType
}}</v-list-item-title>
<v-list-item-subtitle class="text-right">{{
child.AccessionNumber
}}</v-list-item-subtitle>
</v-list-item>
<v-divider />
<v-list-item>
<v-list-item-title
>Protein information</v-list-item-title
>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="proteinLinkFormatter(item.UniProtName)"
><v-icon>fas fa-info</v-icon></v-btn
>
</template>
<span>Information</span>
</v-tooltip>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!item.Expression"
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
@click="
proteinLinkExpressionFormatter(
item.UniProtName
)
"
v-bind="attrs"
v-on="on"
><v-icon>fas fa-street-view</v-icon></v-btn
>
</template>
<span>Expression</span>
</v-tooltip>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!item.BC"
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
proteinLinkBcFormatter(item.UniProtName)
"
>BC</v-btn
>
</template>
<span>Biochemical Assays</span>
</v-tooltip>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
proteinLinkNodeFormatter(item.UniProtName)
"
><v-icon>mdi mdi-apache-kafka</v-icon></v-btn
>
</template>
<span>Interaction Network</span>
</v-tooltip>
</v-list-item>
<v-divider />
<v-list-item>
<v-list-item-title
>Protein analytics</v-list-item-title
>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!item.CurveFit"
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
proteinLinkDsFormatter(item.UniProtName)
"
><v-icon
>mdi mdi-distribute-horizontal-center</v-icon
></v-btn
>
</template>
<span>Dose Selectivity</span>
</v-tooltip>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!item.CurveFit"
:color="
$store.state.selectedOrganismShown
.primaryColor
"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
proteinLinkDsFormatter(item.UniProtName)
"
>CT</v-btn
>
</template>
<span>Combination Treatment</span>
</v-tooltip>
</v-list-item>
</v-list>
</v-expansion-panel-content>
</v-expansion-panel>
</v-expansion-panels>
<v-list-item class="mx-10 py-5">
<v-list-item-title>Combined analytics</v-list-item-title>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!NodeModel.bEnableHeatmap"
:color="$store.state.selectedOrganismShown.primaryColor"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
heatmapLinkFormatter(NodeModel.asUniProtNameHeatmap)
"
><v-icon>mdi mdi-table-column-width</v-icon></v-btn
>
</template>
<span>Interactive Expression Heatmap</span>
</v-tooltip>
<v-tooltip top>
<template v-slot:activator="{ on, attrs }">
<v-btn
:disabled="!NodeModel.bEnableCt"
:color="$store.state.selectedOrganismShown.primaryColor"
outlined
fab
small
class="ma-1"
v-bind="attrs"
v-on="on"
@click="
proteinLinkCtFormatter(NodeModel.asUniProtNameCt)
"
>CT</v-btn
>
</template>
<span>Combination Treatment</span>
</v-tooltip>
</v-list-item>
</v-tab-item>
<v-tab-item :value="'tab-2'">
<v-list-item>
<v-list-item-title class="text-center"
>Visible resources</v-list-item-title
>
</v-list-item>
<v-list dense style="max-height: 400px">
<v-list-item
v-for="(item, i) in GraphRadioModel.Radios"
:key="i"
>
<v-switch
dense
class="ml-7 mt-0 pt-0"
v-model="item.State"
:label="`${item.ResourceType} : ${
!item.State ? 'hidden' : 'visible'
}`"
@change="onRadioSelection"
></v-switch>
</v-list-item>
</v-list>
<v-divider />
<v-col align="center">
<v-list-item>
<v-list-item-title class="text-center"
>Downloadable content</v-list-item-title
>
</v-list-item>
<v-btn
dark
:color="$store.state.selectedOrganismShown.primaryColor"
class="ma-2"
@click="onSvgClick"
><v-icon>fas fa-download</v-icon>SVG</v-btn
>
<v-btn
dark
:color="$store.state.selectedOrganismShown.primaryColor"
class="ma-2"
@click="onPngClick"
><v-icon>fas fa-download</v-icon>PNG</v-btn
>
<v-btn
dark
:color="$store.state.selectedOrganismShown.primaryColor"
class="ma-2"
@click="onSifClick"
><v-icon>fas fa-download</v-icon>SIF</v-btn
>
<canvas id="canvasId" style="display: none"></canvas>
</v-col>
</v-tab-item>
</v-tabs-items>
</v-tabs>
</v-card>
</v-col>
<v-btn
v-if="UiModel.visibleD3Button"
:color="$store.state.selectedOrganismShown.primaryColor"
fab
outlined
elevation="4"
absolute
style="top: 140px; left: 565px"
@click="onButtonPressDelete"
><v-icon>far fa-trash-alt</v-icon></v-btn
>
<v-btn
v-if="UiModel.visibleD3Button"
:color="$store.state.selectedOrganismShown.primaryColor"
:disabled="!UiModel.enableExpansion"
fab
outlined
elevation="4"
absolute
style="top: 210px; left: 565px"
@click="onButtonPressExpand"
><v-icon>fas fa-plus</v-icon></v-btn
>
<v-btn
v-if="UiModel.visibleD3Button"
:color="$store.state.selectedOrganismShown.primaryColor"
fab
outlined
elevation="4"
absolute
style="top: 280px; left: 565px"
@click="onButtonPressUnfix"
><v-icon>fas fa-unlock-alt</v-icon></v-btn
>
<v-col cols="9">
<interactiongraph
ref="interactionsgraph"
v-if="UiModel.visibleD3Button"
:height="'600px'"
:proteinId="proteinId"
:selectedEdges="SelectionModel"
@visibleRetrieval="onRetrievalChange"
:accessionId="PlotInformationModel.AccessionId"
:sRelationTypeIds="PlotInformationModel.sRelationTypeIds"
:endpointAccession="
$store.state.host +
'/proteomicsdb/logic/pathways/getAccessionId.xsjs?protein_id=__parameter1__'
"
:endpointMarker="
$store.state.host +
'/proteomicsdb/logic/pathways/getAllMarkers.xsjs'
"
:endpointSuperNodeInfo="
$store.state.host +
'/proteomicsdb/logic/pathways/getSuperNodeInfo.xsjs'
"
@disableNodeTab="disableNodeTab"
@keyChange="onKeyChange"
@showOverlay="onShowOverlay"
@enableExpansion="onEnableExpansion"
@triggerRadioSelection="onRadioSelection"
@NodeModel="onNodeSelection"
@radioButtons="setGraphRadioModel"
:heatmapLinkGenerator="heatmapLinkFormatter"
:endpoint="
this.$store.state.host +
'/proteomicsdb/logic/pathways/getPathwayGraphForProteinId.xsjs?accession_id=__parameter1__&resource_type=__parameter2__&relation_ids=__parameter3__&offset=__parameter4__&new_graph=__parameter5__&sn_exist=__parameter6__'
"
/>
</v-col>
<edgePopup
:openDialog="isEdgeSelected"
:inputData="overlayData"
@closePopUp="disablePopUp"
/>
</v-row>
</v-container>
</template>
<script>
import axios from "axios";
import utils from "@/vue-d3-component-wrappers/common-lib/Utils.js";
import edgePopup from "@/views/popup/InteractionNetworkEdgeOverlay";
import interactiongraph from "@/vue-d3-components/InteractionNetwork";
import router from "@/router";
export default {
name: "proteinInteractionGraph",
components: {
interactiongraph: interactiongraph,
edgePopup: edgePopup,
},
props: {
minWidth: {
type: Number,
default: 400,
},
minHeight: {
type: Number,
default: 400,
},
proteinId: {
type: String,
default: null,
},
proteinAccession: {
type: String,
default: null,
},
},
data: function () {
return {
RelationTypesModel: [],
isNodeSelected: false,
isEdgeSelected: false,
isGraphShown: false,
loader: null,
loading: false,
tab: 0,
PlotInformationModel: {
proteinId: this.proteinId,
visible: false,
},
overlayData: [
{
Source: "",
Destination: "",
Relations: [],
},
{
Source: "",
Destination: "",
Relations: [],
},
],
UiModel: {
visibleD3Button: false,
visibleEdge: false,
visibleNode: false,
tabIndex: "tab-0",
isRendered: false,
visibleRetrieval: false,
canvasHidden: "<canvas id=hiddenPNG style=display:none />",
},
SelectionModel: [],
GraphRadioModel: { Radios: [] },
NodeModel: [],
modifiedRelationSelection: false,
svgCss: [
require("@/vue-d3-components/d3v4-selectable-zoomable-force-directed-graph.css.prdb"),
],
};
},
watch: {
/* loader () {
const l = this.loader
this[l] = !this[l]
setTimeout(() => (this[l] = false), 3000)
this.loader = null
},*/
},
methods: {
getAccessionId: function () {
var that = this;
axios
.get(
this.$store.state.host +
"/proteomicsdb/logic/pathways/getAccessionId.xsjs",
{ params: { protein_id: that.proteinId } }
)
.then(function (response) {
that.PlotInformationModel.AccessionId = response.data.AccessionId;
});
},
getRelations: function () {
var that = this;
this.modifiedRelationSelection = true;
axios
.get(
this.$store.state.host +
"/proteomicsdb/logic/pathways/getAllRelationTypes.xsjs",
{}
)
.then(function (response) {
var aRelationTypes = response.data;
aRelationTypes = aRelationTypes.map(function (dataset) {
dataset.Children = dataset.Children.map(function (elements) {
elements.value = elements.Name;
elements.selected = elements.Selected > 0;
elements.cheatCss = "sapInteractionCheckbox" + elements.Level;
var xDistance = elements.Level * 30 + 10;
var svgConstructStart =
'<svg height="21" width="' + xDistance + '">';
var svgConstructStop = "</svg>";
// CHEAT is necessary for unique ids in the document
var marker_base =
'<marker id="CHEAT__ArrowTypeId__" viewBox="-10 -10 20 20" refX="0" refY="0" markerWidth="6" markerHeight="6" orient="auto"><path transform="scale(1)" fill="__ArrowColour__" d="__Marker__"></path></marker>';
var marker = elements.EndArrowTypeId
? marker_base
.replace("__ArrowTypeId__", elements.EndArrowTypeId)
.replace("__ArrowColour__", elements.EndArrowColour)
.replace("__Marker__", elements.EndMarker)
: "";
marker += elements.StartArrowTypeId
? marker_base
.replace("__ArrowTypeId__", elements.StartArrowTypeId)
.replace("__ArrowColour__", elements.StartArrowColour)
.replace("__Marker__", elements.StartMarker)
: "";
marker += elements.MidArrowTypeId
? marker_base
.replace("__ArrowTypeId__", elements.MidArrowTypeId)
.replace("__ArrowColour__", elements.MidArrowColour)
.replace("__Marker__", elements.MidMarker)
: "";
var defs = "<defs>" + marker + "</defs>";
var marker_mid = elements.MidArrowTypeId
? ' marker-mid="url(#CHEAT__MidArrowTypeId__)" '.replace(
"__MidArrowTypeId__",
elements.MidArrowTypeId
)
: "";
var marker_end = elements.EndArrowTypeId
? ' marker-end="url(#CHEAT__EndArrowTypeId__)" '.replace(
"__EndArrowTypeId__",
elements.EndArrowTypeId
)
: "";
var marker_start = elements.StartArrowTypeId
? ' marker-mid="url(#CHEAT__StartArrowTypeId__)" '.replace(
"__StartArrowTypeId__",
elements.StartArrowTypeId
)
: "";
var path_base =
"<path " +
marker_mid +
marker_end +
marker_start +
' class="linkRef" refY="-50" stroke="black" stroke-width="3px" d="M10,10L20,10L30,10"></path>';
var path = path_base.replace(
"__ArrowTypeId__",
elements.ArrowTypeId
);
elements.svg = svgConstructStart + defs + path + svgConstructStop;
return elements;
});
return dataset;
});
that.RelationTypesModel = aRelationTypes;
});
},
disablePopUp: function () {
this.isEdgeSelected = false;
},
onEnableExpansion: function onEnableExpansion(oEvent) {
var bEnable = oEvent.bEnable;
this.UiModel.enableExpansion = bEnable;
},
runAnalysis: function () {
if (this.modifiedRelationSelection) {
this.loader = "loading";
const l = this.loader;
this[l] = !this[l];
this.modifiedRelationSelection = false;
}
this.UiModel.visibleD3Button = true;
this.UiModel.visibleEdge = false;
this.UiModel.visibleNode = false;
this.UiModel.tabIndex = "tab-0";
this.UiModel.isRendered = false;
this.UiModel.visibleRetrieval = false;
var sRelationTypeIds = this.getSelectedRelationTypeIds();
this.PlotInformationModel.sRelationTypeIds = sRelationTypeIds;
this.PlotInformationModel.visible = true;
this.$emit("dataLoaded", null);
},
onRetrievalChange: function (data) {
this.UiModel.visibleRetrieval = data.value;
const l = this.loader;
this[l] = false;
this.loader = null;
},
onKeyChange: function onKeyChange(oEvent) {
var iTabId = oEvent.iTabId;
this.UiModel.visibleEdge = iTabId === 1 ? false : true;
this.UiModel.visibleNode = iTabId === 2 ? false : true;
this.UiModel.tabIndex = "tab-" + iTabId;
},
nTitleFormatter: function proteinTitleFormatter(name, id) {
return name + " (" + id + ")";
},
onCheckBoxChange: function onCheckBoxChange() {},
disableNodeTab: function disableNodeTab(oEvent) {
var bDisableNode = oEvent.bDisable;
this.UiModel.visibleNode = !bDisableNode;
this.NodeModel = [];
if (this.UiModel.tabIndex === "tab-1") {
this.UiModel.tabIndex = "tab-0";
this.UiModel.enableExpansion = false;
}
},
onShowOverlay: function onShowOverlay(oEvent) {
var sSource = oEvent.source;
var sTarget = oEvent.target;
var sDirectional = oEvent.directional;
var sArrowType = oEvent.arrowtype;
var sRelation_ids = oEvent.relation_ids;
var that = this;
axios
.get(
this.$store.state.host +
"/proteomicsdb/logic/pathways/getEdgeInfo.xsjs",
{
params: {
source: sSource,
target: sTarget,
directional: sDirectional,
arrowtype: sArrowType,
relation_ids: sRelation_ids,
},
}
)
.then(function (response) {
that.overlayData = response.data;
that.isEdgeSelected = true;
});
},
onSelectionModelChange: function onSelectionModelChange() {},
onButtonNetwork: function onButtonNetwork() {
//I have the vague feeling that this is not doing anything...
window.open("tesgt", "_blank");
},
onButtonPressExpand: function onButtonPressExpand() {
this.$refs.interactionsgraph.expandSelection();
},
onButtonPressDelete: function onButtonPressDelete() {
this.$refs.interactionsgraph.deleteSelectionDirty();
},
onButtonPressUnfix: function onButtonPressUnfix() {
this.$refs.interactionsgraph.unfixSelection();
},
onSvgClick: function () {
var aPlots = [];
aPlots.push(this.$refs.interactionsgraph.getSVG());
utils.downloadSVGs(
aPlots,
"InteractionsGraph: ",
true,
"canvasId",
this.svgCss
);
},
onPngClick: function () {
var aPlots = [];
aPlots.push(this.$refs.interactionsgraph.getSVG());
utils.downloadSVGs(
aPlots,
"InteractionsGraph: ",
false,
"canvasId",
this.svgCss
);
},
onSifClick: function () {
var aCSVRows = this.$refs.interactionsgraph.getSif();
var sFileName = this.proteinAccession;
utils.downloadFile(aCSVRows, sFileName, "sif");
},
proteinLinkFormatter: function proteinLinkFormatter(iProteinId) {
router.push("/vue/protein/" + iProteinId + "/summary");
},
proteinLinkBcFormatter: function proteinLinkBcFormatter(iProteinId) {
router.push("/vue/protein/" + iProteinId + "/assay");
},
proteinLinkNodeFormatter: function proteinLinkNodeFormatter(iProteinId) {
router.push("/vue/protein/" + iProteinId + "/interactions");
},
proteinLinkExpressionFormatter: function proteinLinkExpressionFormatter(
iProteinId
) {
router.push("/vue/protein/" + iProteinId + "/expression");
},
proteinLinkCtFormatter: function proteinLinkCtFormatter(asUniProtName) {
if (typeof asUniProtName === "string") {
router.push(
"/vue/analytics/combinationTreatment?protein_name=" + asUniProtName
);
} else if (typeof asUniProtName === "undefined") {
return "";
}
router.push(
"/vue/analytics/combinationTreatment?protein_name=" +
asUniProtName.join(",")
);
},
proteinLinkDsFormatter: function proteinLinkDsFormatter(sUniProtName) {
router.push(
"/vue/analytics/selectivity?protein_name=" + sUniProtName
);
},
// array consists of Data from D3 graph
heatmapLinkFormatter: function heatmapLinkFormatter(asUniProtNameHeatmap) {
if (typeof asUniProtNameHeatmap === "undefined") {
return "";
}
var iTaxCode = this.$store.state.cookie;
router.push(
"/vue/analytics/expressionHeatmap?proteins=" +
asUniProtNameHeatmap.join("%3B") +
"&quantification=1&biologicalSource=tissue%3Bfluid&calculationMethod=0&swissprotOnly=1&noIsoforms=1&taxcode=" +
iTaxCode
);
},
setGraphRadioModel: function (oData) {
this.GraphRadioModel.Radios = oData;
},
onRadioSelection: function onRadioSelection() {
var aRadioStuff = this.GraphRadioModel.Radios;
var aShownShapes = aRadioStuff
.filter(function (d) {
return d.State;
})
.map(function (d) {
return d.Shape;
});
this.$refs.interactionsgraph.seek_and_hide(true, aShownShapes);
},
onNodeSelection: function (nodes) {
this.NodeModel = nodes;
},
getSelectedRelationTypeIds: function getSelectedRelationTypeIds() {
var aRelationTypes = this.RelationTypesModel;
aRelationTypes = aRelationTypes.map(function (dataset) {
var selectedElements = dataset.Children.filter(function (element) {
return element.selected;
});
return selectedElements.map(function (element) {
return element.RelationTypeId;
});
});
return aRelationTypes
.reduce(function (a, b) {
return a.concat(b);
}, [])
.join(",");
},
},
computed: {
selectedRelations: function () {
var aRelationTypes = this.RelationTypesModel;
aRelationTypes = aRelationTypes.map(function (dataset) {
var selectedElements = dataset.Children.filter(function (element) {
return element.selected;
});
return selectedElements.map(function (element) {
return element.RelationTypeId;
});
});
return aRelationTypes
.reduce(function (a, b) {
return a.concat(b);
}, [])
.join(",");
},
},
mounted() {
this.getRelations();
this.getAccessionId();
},
};
</script>
<style scss>
@import "../vue-d3-components/d3v4-selectable-zoomable-force-directed-graph.css.prdb";
</style>