nightingale-sequence-heatmap

Nightingale Sequence Heatmap component is used to generate a heatmap visualisation with residue bound data.

It uses heatmap-component to render the canvas heatmap.

Attributes

hm-highlight-width: number (default 0)

Number of pixels for the border width of the heatmap. See live demos for examples with border width 1.

Usage

The below example shows how to instantiate the component

<nightingale-sequence-heatmap
  id="id-for-nightingale-sequence-heatmap"
  heatmap-id="seq-heatmap"
  width="400"
  height="400"
  hm-highlight-width="0"
  highlight-event="onmouseover"
  highlight-color="#EB3BFF66"
></nightingale-sequence-heatmap>

Please note that after instantiation the component needs to be initialized using the setHeatmapData function as seem below:

const xDomain = [1, 2, 3]; // 1-indexed residue ids
const yDomain = ["A", "B", "C"]; // categories (rows) to show on heatmap
const data = [
  // array of objects to be displayed, see more info on API Reference
  { xValue: 1, yValue: "A", score: 0.4 },
  { xValue: 1, yValue: "B", score: 32 },
  { xValue: 1, yValue: "C", score: 1.6 },
  { xValue: 2, yValue: "A", score: 2.5 },
  { xValue: 2, yValue: "B", score: 1 },
  { xValue: 2, yValue: "C", score: 7.6 },
  { xValue: 3, yValue: "A", score: 25.0 },
  { xValue: 3, yValue: "B", score: 10 },
  { xValue: 3, yValue: "C", score: 6 },
];
customElements.whenDefined("nightingale-sequence-heatmap").then(() => {
  document
    .getElementById("id-for-nightingale-sequence-heatmap")
    .setHeatmapData(xDomain, yDomain, data); // initialization function
});

API Reference

Properties

setHeatmapData(xDomain: number[], yDomain: string[], data: Array)

The data array is of the HotmapData structure.

Please note that this format is flexible to additional properties for specific use cases ([key: string]: any;)

interface HotmapData {
  xValue: number; // residue index (columns)
  yValue: string; // category type (rows)
  score: number; // heatmap value converted to colors
  [key: string]: unknown; // additional properties for specific use cases such as custom tooltips
}

Heatmap-component Reference

Useful functions

setColor((d: HotmapData) => {})

Allows dynamic setting of heatmap color palette

customElements.whenDefined("nightingale-sequence-heatmap").then( async() => {
  const heatmapElement = document.getElementById(
    "id-for-nightingale-sequence-heatmap",
  );
  heatmapElement.setHeatmapData(xDomain, yDomain, data);

  const colorScale = d3.scaleLinear(
    [0, 1], // score value domain
    ["#ffffff", "#00441b"], // color range to map values
  );

  await heatmapElement.updateComplete.then(() => {
    heatmapElement.heatmapInstance.setColor((d) => colorScale(d.score));
  });
});

setTooltip((d: HotmapData, x: number, y: number, xIndex: number, yIndex: number) => {})

Allows dynamic setting of tooltip HTML content

customElements.whenDefined("nightingale-sequence-heatmap").then( async() => {
  const heatmapElement = document.getElementById(
    "id-for-nightingale-sequence-heatmap",
  );
  heatmapElement.setHeatmapData(xDomain, yDomain, data);
  
  await heatmapElement.updateComplete.then(() => {
    heatmapElement.heatmapInstance.setTooltip((d, x, y, xIndex, yIndex) => {
      let returnHTML = `
        <b>You are at</b> <br />

        x,y: <b>${d.xValue},${d.yValue}</b><br />
        score: <b>${d.score}</b>`;
      return returnHTML;
    });
  });
});