grnsight 3.0.0 → 5.1.0

package/web-client/public/js/grnstate.js

@@ -0,0 +1,147 @@
+import { max } from "d3-array";
+import {
+  SHOW_WEIGHTS_MOUSEOVER,
+  LINK_DIST_SLIDER_SIDEBAR,
+  LINK_DIST_VALUE,
+  LINK_DIST_DEFAULT_VALUE,
+  CHARGE_SLIDER_SIDEBAR,
+  CHARGE_VALUE,
+  CHARGE_DEFAULT_VALUE,
+  DEFAULT_MAX_LOG_FOLD_CHANGE,
+  DEFAULT_ZOOM_VALUE,
+  FORCE_GRAPH,
+  VIEWPORT_INIT
+} from "./constants";
+let currentWorkbook = null;
+
+const annotateLinks = workbook => {
+    // TODO This duplicates logic that is done on the server side for an .xlsx spreadsheet.
+    //      Think of a way to consolidate it. Having discovered this, it seems like this should
+    //      be done on the client side because it rearranges data redundantly, for ease of display.
+    workbook.positiveWeights = [];
+    workbook.negativeWeights = [];
+
+    workbook.links.forEach(link => {
+        if (workbook.sheetType === "unweighted" && !link.value) {
+            link.value = 1;
+        }
+
+        if (link.value > 0) {
+            link.type = "arrowhead";
+            // link.stroke = "MediumVioletRed";   // GRNsight v1 magenta edge color
+            link.stroke = "rgb(195, 61, 61)";     // Node coloring-consistent red edge color
+            workbook.positiveWeights.push(link.value);
+        } else {
+            link.type = "repressor";
+            // link.stroke = "DarkTurquoise";     // GRNsight v1 cyan edge color
+            link.stroke = "rgb(51, 124, 183)";    // Node coloring-consistent blue edge color
+            workbook.negativeWeights.push(link.value);
+        }
+    });
+};
+
+export const grnState = {
+    name: null,
+    simulation: undefined,
+    newWorkbook: false,
+
+    get workbook () {
+        return currentWorkbook;
+    },
+
+    set workbook (workbook) {
+        currentWorkbook = workbook;
+        // TODO: add colorOptimal so that the rest of the normalization code can get added
+        this.resetNormalizationMax = max(workbook.positiveWeights.concat(workbook.negativeWeights));
+        this.newWorkbook = true;
+    },
+
+// Edge Display Parameters
+    normalizationMax: null,
+    resetNormalizationMax: null,
+    edgeWeightDisplayOption: SHOW_WEIGHTS_MOUSEOVER,
+    colorOptimal: true,
+    grayEdgeThreshold: 5,
+    dashedLine: false,
+
+    annotateLinks: () => annotateLinks(currentWorkbook),
+
+// Zoom Parameter
+    zoomValue: DEFAULT_ZOOM_VALUE,
+
+// Node Coloring
+    nodeColoring: {
+        showMenu: false,
+        nodeColoringEnabled: true,
+        logFoldChangeMaxValue: DEFAULT_MAX_LOG_FOLD_CHANGE,
+        logFoldChangeUpdateTriggered: false,
+        averageTopDataset: true,
+        averageBottomDataset: true,
+        topDataset: undefined,
+        bottomDataset: undefined,
+        lastDataset: null,
+        bottomDataSameAsTop: true,
+        nodeColoringOptions: [],
+    },
+
+
+// Gene Page data
+// left defaulting to yeast for tests, until a better solution is found
+// Setting base case to yeast
+    genePageData: {
+        commonName: "Yeast",
+        species: "Saccharomyces_cerevisiae",
+        taxonUniprot: "559292",
+        taxonJaspar: "4932",
+        identified: false,
+        ensembl: "reg",
+        mine: "yeast"
+    },
+
+    nameToTaxon: {
+        // Treating like a dictionary with keys being the english name
+        // and values being a dictionary of (latin name, Uniprot, Jaspar)
+        // some taxon ids are different between the two
+        // changed spec names for common english and will have them formatted before calling an api
+        "Arabidopsis thaliana": { spec: "Arabidopsis_thaliana", jaspar: 3702, uniprot: 3702,
+            ensembl: "plant", mine: "thale"},
+        "Caenorhabditis elegans": { spec: "Caenorhabditis_elegans", jaspar: 6293, uniprot: 6293,
+            ensembl: "reg", mine: "worm"},
+        "Drosophila melanogaster": { spec: "Drosophila_melanogaster", jaspar: 7227, uniprot: 7227,
+            ensembl: "reg", mine: "fly"},
+        "Homo sapiens": { spec: "Homo_sapiens", jaspar: 9606, uniprot: 9606, ensembl: "reg",
+            mine: "fly"},
+        "Mus musculus": { spec: "Mus_musculus", jaspar: 10090, uniprot: 10090, ensembl: "reg",
+            mine: "mouse"},
+        "Saccharomyces cerevisiae": { spec: "Saccharomyces_cerevisiae", jaspar: 4932, uniprot: 559292,
+            ensembl: "reg", mine: "yeast"}
+    },
+
+// Slider Parameters
+    slidersLocked: false,
+    showUndoReset: false,
+    linkDistanceSlider: {
+        sliderId: LINK_DIST_SLIDER_SIDEBAR,
+        valueId: LINK_DIST_VALUE,
+        defaultVal: LINK_DIST_DEFAULT_VALUE,
+        currentVal: LINK_DIST_DEFAULT_VALUE,
+        backup: LINK_DIST_DEFAULT_VALUE,
+        needsAppendedZeros: false,
+        forceChanged: false,
+    },
+    chargeSlider: {
+        sliderId: CHARGE_SLIDER_SIDEBAR,
+        valueId: CHARGE_VALUE,
+        defaultVal: CHARGE_DEFAULT_VALUE,
+        currentVal: CHARGE_DEFAULT_VALUE,
+        backup: CHARGE_DEFAULT_VALUE,
+        needsAppendedZeros: false,
+        forceChanged: false,
+    },
+
+// Graph Layout Parameter
+    graphLayout: FORCE_GRAPH,
+
+// Viewport Size Parameter
+    viewportSize: VIEWPORT_INIT,
+};

package/web-client/public/js/iframe-coordination.js

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+/* eslint-disable */
+// ^^^^^ Disabled because this code is meant to be run in the host website and explicitly relies
+//       on top-level names like iFrameResize and jQuery ($).
+
+/**
+ * This script is for use by the top-level GRNsight website, in order to coordinate sizing between the
+ * host site and the embedded GRNsight application. It is meant to be executed _in the host site_
+ * via a standard `script` element.
+ *
+ * Prerequisites: jQuery and the iFrame Resizer library (v4.1.1 at this writing) must already be
+ *                loaded into the web browser when this script executes.
+ */
+iFrameResize({
+  checkOrigin: ["https://dondi.github.io", "https://grnsight.cs.lmu.edu"],
+  widthCalculationMethod: "taggedElement",
+  heightCalculationMethod: "taggedElement",
+  sizeWidth: true,
+  minWidth: 1081  // Based on minimum width page body and title elements.
+}, "iframe.embedded-demo");
+
+const HEIGHT_OFFSET = 53;
+const HEIGHT_PADDING = 20;
+
+const SMALL_HEIGHT = 648 + HEIGHT_OFFSET;
+const MEDIUM_HEIGHT = 840 + HEIGHT_OFFSET;
+const LARGE_HEIGHT = 1080 + HEIGHT_OFFSET;
+const FIT_MARGIN = 4;  // A little space so that "fit" isn’t totally flush with window bounds.
+
+const sendDimensions = (destination, origin) => {
+  const iframeOffset = $("iframe.embedded-demo").offset();
+  destination.postMessage(
+    {
+      width: $(window).width() - iframeOffset.left,
+      height: $(window).height() - FIT_MARGIN,
+      top: iframeOffset.top
+    },
+
+    origin
+  );
+};
+
+window.addEventListener("message", event => {
+  if (event.origin.indexOf("https://grnsight.cs.lmu.edu") !== 0) {
+    // Ignore any message that did not originate from the GRNsight web client server.
+    return;
+  }
+
+  if (event.data === "dimensions") {
+    sendDimensions(event.source, event.origin);
+  }
+});
+
+window.addEventListener("resize", () => sendDimensions(
+  document.querySelector("iframe.embedded-demo").contentWindow, "https://grnsight.cs.lmu.edu"
+));