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wip-x-axis #612

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e8000e0
wip-x-axis
theosanderson Sep 26, 2024
c015532
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 26, 2024
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2 changes: 1 addition & 1 deletion taxonium_component/src/components/Key.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ const Key = ({
</h3>

{!collapsed &&
((colorRamps && colorByField in colorRamps) ? (
(colorRamps && colorByField in colorRamps ? (
<ColorRamp ramp={colorRamps[colorByField]} />
) : (
<KeyContent
Expand Down
146 changes: 117 additions & 29 deletions taxonium_component/src/hooks/useLayers.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,33 @@ import { useMemo, useCallback } from "react";
import useTreenomeLayers from "./useTreenomeLayers";
import getSVGfunction from "../utils/deckglToSvg";

// Function to calculate "nice" tick values
const generateNiceTicks = (min, max, maxTicks) => {
const range = max - min;
const roughTickSize = range / (maxTicks - 1);
const orderOfMagnitude = Math.floor(Math.log10(roughTickSize));
const pow10 = Math.pow(10, orderOfMagnitude);

const possibleTickSizes = [1, 2, 5, 10];
let tickSize = possibleTickSizes[0] * pow10;
for (let i = 0; i < possibleTickSizes.length; i++) {
tickSize = possibleTickSizes[i] * pow10;
if (range / tickSize <= maxTicks) {
break;
}
}

const niceMin = Math.floor(min / tickSize) * tickSize;
const niceMax = Math.ceil(max / tickSize) * tickSize;

const ticks = [];
for (let x = niceMin; x <= niceMax; x += tickSize) {
ticks.push(x);
}

return ticks;
};

const getKeyStuff = (getNodeColorField, colorByField, dataset, toRGB) => {
const counts = {};
for (const node of dataset.nodes) {
Expand Down Expand Up @@ -160,10 +187,6 @@ const useLayers = ({
getPosition: (d) => [getX(d), d.y],
getFillColor: (d) => toRGB(getNodeColorField(d, detailed_data)),
getRadius: settings.nodeSize,
// radius in pixels
// we had to get rid of the below because it was messing up the genotype colours
// getRadius: (d) =>
// getNodeColorField(d, detailed_data) === hoveredKey ? 4 : 3,
getLineColor: [100, 100, 100],
opacity: settings.opacity,
stroked: data.data.nodes && data.data.nodes.length < 3000,
Expand Down Expand Up @@ -193,9 +216,7 @@ const useLayers = ({
selectedDetails.nodeDetails.node_id === d.node_id
? 3.5
: 1,

onHover: (info) => setHoverInfo(info),

modelMatrix: modelMatrix,
updateTriggers: {
getSourcePosition: [detailed_data, xType],
Expand Down Expand Up @@ -285,16 +306,12 @@ const useLayers = ({
opacity: 1,
getRadius: 6,
radiusUnits: "pixels",

id: "main-selected",
filled: false,
stroked: true,
modelMatrix,

getLineColor: [0, 0, 0],
getPosition: (d) => {
return [d[xType], d.y];
},
getPosition: (d) => [d[xType], d.y],
lineWidthUnits: "pixels",
lineWidthScale: 2,
};
Expand All @@ -306,16 +323,12 @@ const useLayers = ({
opacity: 0.3,
getRadius: 4,
radiusUnits: "pixels",

id: "main-hovered",
filled: false,
stroked: true,
modelMatrix,

getLineColor: [0, 0, 0],
getPosition: (d) => {
return [d[xType], d.y];
},
getPosition: (d) => [d[xType], d.y],
lineWidthUnits: "pixels",
lineWidthScale: 2,
};
Expand All @@ -327,12 +340,10 @@ const useLayers = ({
data: clade_data,
getPosition: (d) => [getX(d), d.y],
getText: (d) => d.clades[clade_accessor],

getColor: settings.cladeLabelColor,
getAngle: 0,
fontFamily: "Roboto, sans-serif",
fontWeight: 700,

billboard: true,
getTextAnchor: "end",
getAlignmentBaseline: "center",
Expand Down Expand Up @@ -377,10 +388,8 @@ const useLayers = ({
),
getPosition: (d) => [getX(d), d.y],
getText: (d) => d[config.name_accessor],

getColor: settings.terminalNodeLabelColor,
getAngle: 0,

billboard: true,
getTextAnchor: "start",
getAlignmentBaseline: "center",
Expand All @@ -399,10 +408,8 @@ const useLayers = ({
getPolygonOffset: ({ layerIndex }) => [0, -4000],
getPosition: (d) => [getX(d), d.y],
getFillColor: (d) => toRGB(getNodeColorField(d, base_data)),
// radius in pixels
getRadius: 2,
getLineColor: [100, 100, 100],

opacity: 0.6,
radiusUnits: "pixels",
onHover: (info) => setHoverInfo(info),
Expand Down Expand Up @@ -434,7 +441,6 @@ const useLayers = ({
getSourcePosition: (d) => [d.parent_x, d.y],
getTargetPosition: (d) => [d.parent_x, d.parent_y],
getColor: lineColor,

updateTriggers: {
getSourcePosition: [base_data, xType],
getTargetPosition: [base_data, xType],
Expand All @@ -451,7 +457,6 @@ const useLayers = ({
opacity: 0.3,
filled: true,
getPolygonOffset: ({ layerIndex }) => [0, -2000],

getFillColor: (d) => [255, 255, 255],
};

Expand All @@ -478,12 +483,10 @@ const useLayers = ({
const data = searchResults[spec.key]
? searchResults[spec.key].result.data
: [];

const lineColor = search.getLineColor(i);

return {
layerType: "ScatterplotLayer",

data: data,
id: "main-search-scatter-" + spec.key,
getPosition: (d) => [d[xType], d.y],
Expand Down Expand Up @@ -526,20 +529,104 @@ const useLayers = ({
radiusUnits: "pixels",
lineWidthUnits: "pixels",
stroked: true,

wireframe: true,
getLineWidth: 1,
filled: false,
getFillColor: [255, 0, 0, 0],
updateTriggers: { getPosition: [xType] },
};
});
layers.push(...search_layers, ...search_mini_layers);

layers.push(...search_layers, ...search_mini_layers);
layers.push(minimap_polygon_background);
layers.push(minimap_line_horiz, minimap_line_vert, minimap_scatter);
layers.push(minimap_bound_polygon);

// Add x-axis layers with intelligent tick values
const xAxisLayers = useMemo(() => {
// Determine x-axis position
const xAxisY =
viewState.min_y < -1000
? -1000
: viewState.max_y - (viewState.max_y - viewState.min_y) * 0.05;

// Determine x-axis range
const xAxisMinX = viewState.min_x;
const xAxisMaxX = viewState.max_x;

// Decide on the maximum number of ticks
const maxTicks = 10;

// Generate nice tick positions
const tickPositions = generateNiceTicks(xAxisMinX, xAxisMaxX, maxTicks);

// Axis line layer
const xAxisLineLayer = {
layerType: "LineLayer",
id: "x-axis-line",
data: [
{
sourcePosition: [tickPositions[0], xAxisY],
targetPosition: [tickPositions[tickPositions.length - 1], xAxisY],
},
],
getSourcePosition: (d) => d.sourcePosition,
getTargetPosition: (d) => d.targetPosition,
getColor: [0, 0, 0],
getWidth: 2,
widthUnits: "pixels",
modelMatrix: modelMatrix,
updateTriggers: {
getSourcePosition: [tickPositions[0], xAxisY],
getTargetPosition: [tickPositions[tickPositions.length - 1], xAxisY],
},
};

// Tick marks layer
const xAxisTickMarksLayer = {
layerType: "LineLayer",
id: "x-axis-ticks",
data: tickPositions.map((x) => ({
sourcePosition: [x, xAxisY],
targetPosition: [x, xAxisY - 10], // Adjust the tick length as needed
})),
getSourcePosition: (d) => d.sourcePosition,
getTargetPosition: (d) => d.targetPosition,
getColor: [0, 0, 0],
getWidth: 1,
widthUnits: "pixels",
modelMatrix: modelMatrix,
updateTriggers: {
data: [tickPositions, xAxisY],
},
};

// Tick labels layer
const xAxisLabelsLayer = {
layerType: "TextLayer",
id: "x-axis-labels",
data: tickPositions.map((x) => ({
position: [x, xAxisY - 15], // Position labels below the tick marks
text: x.toFixed(2), // Format the x-value as needed
})),
getPosition: (d) => d.position,
getText: (d) => d.text,
getColor: [0, 0, 0],
getSize: 12,
getTextAnchor: "middle",
getAlignmentBaseline: "top",
modelMatrix: modelMatrix,
updateTriggers: {
data: [tickPositions, xAxisY],
},
};

return [xAxisLineLayer, xAxisTickMarksLayer, xAxisLabelsLayer];
}, [viewState.min_x, viewState.max_x, viewState.min_y, modelMatrix]);

// Add the x-axis layers to the layers array
layers.push(...xAxisLayers);

const layerFilter = useCallback(
({ layer, viewport, renderPass }) => {
const first_bit =
Expand All @@ -552,7 +639,8 @@ const useLayers = ({
viewport.id === "browser-main") ||
(layer.id.startsWith("browser-fillin") &&
viewport.id === "browser-main" &&
isCurrentlyOutsideBounds);
isCurrentlyOutsideBounds) ||
(layer.id.startsWith("x-axis") && viewport.id === "main");

return first_bit;
},
Expand Down
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