diff --git a/v3/src/components/data-display/d3-types.ts b/v3/src/components/data-display/d3-types.ts
index c815f9011f..8c1499f291 100644
--- a/v3/src/components/data-display/d3-types.ts
+++ b/v3/src/components/data-display/d3-types.ts
@@ -1,2 +1,5 @@
  // The data stored with each plot element (e.g. 'circle')
 export type CaseData = { plotNum: number, caseID: string }
+
+// The data stored with each plot element (e.g. 'circle') when subplots are used
+export type CaseDataWithSubPlot = { plotNum: number; caseID: string; subPlotNum?: number }
diff --git a/v3/src/components/data-display/data-display-utils.ts b/v3/src/components/data-display/data-display-utils.ts
index 41368328d7..e02eb8b000 100644
--- a/v3/src/components/data-display/data-display-utils.ts
+++ b/v3/src/components/data-display/data-display-utils.ts
@@ -7,6 +7,7 @@ import {
 } from "../../utilities/color-utils"
 import {between} from "../../utilities/math-utils"
 import { IBarCover } from "../graph/graphing-types"
+import {isGraphDataConfigurationModel} from "../graph/models/graph-data-configuration-model"
 import {ISetPointSelection} from "../graph/utilities/graph-utils"
 import {
   hoverRadiusFactor, kDataDisplayFont, Point, PointDisplayType, pointRadiusLogBase, pointRadiusMax, pointRadiusMin,
@@ -14,6 +15,7 @@ import {
 } from "./data-display-types"
 import {IDataConfigurationModel } from "./models/data-configuration-model"
 import {IPixiPointStyle, PixiPoints} from "./pixi/pixi-points"
+import {CaseDataWithSubPlot} from "./d3-types"
 
 export const maxWidthOfStringsD3 = (strings: Iterable<string>) => {
   let maxWidth = 0
@@ -85,7 +87,9 @@ export interface IMatchCirclesProps {
 export function matchCirclesToData(props: IMatchCirclesProps) {
   const { dataConfiguration, pixiPoints, startAnimation, pointRadius, pointColor, pointStrokeColor,
           pointDisplayType = "points" } = props
-  const allCaseData = dataConfiguration.joinedCaseDataArrays
+  const allCaseData: CaseDataWithSubPlot[] = isGraphDataConfigurationModel(dataConfiguration)
+    ? dataConfiguration.caseDataWithSubPlot
+    : dataConfiguration.joinedCaseDataArrays
 
   startAnimation()
 
@@ -212,4 +216,3 @@ export function rectToTreeRect(rect: Rect) {
     h: rect.height
   }
 }
-
diff --git a/v3/src/components/data-display/hooks/use-connecting-lines.ts b/v3/src/components/data-display/hooks/use-connecting-lines.ts
index 8b0de48125..556afc2f5e 100644
--- a/v3/src/components/data-display/hooks/use-connecting-lines.ts
+++ b/v3/src/components/data-display/hooks/use-connecting-lines.ts
@@ -73,7 +73,7 @@ export const useConnectingLines = (props: IProps) => {
 
   const handleConnectingLinesMouseOver = useCallback((mouseOverProps: IMouseOverProps) => {
     const { caseIDs, event, parentAttrName, primaryAttrValue } = mouseOverProps
-    if (pixiPoints) pixiPoints.canvas.style.cursor = "pointer"
+    if (pixiPoints?.canvas) pixiPoints.canvas.style.cursor = "pointer"
     // TODO: In V2, the tool tip is only shown when there is a parent attribute. V3 should always show the tool tip,
     // but the text needs to be different when there is no parent attribute. We'll need to work out how to handle the
     // localization for this. When a parent attribute is present, the tool tip should look like:
@@ -90,7 +90,7 @@ export const useConnectingLines = (props: IProps) => {
   }, [dataTip, dataset?.name, pixiPoints])
 
   const handleConnectingLinesMouseOut = useCallback(() => {
-    if (pixiPoints) pixiPoints.canvas.style.cursor = ""
+    if (pixiPoints?.canvas) pixiPoints.canvas.style.cursor = ""
     dataTip.hide()
   }, [dataTip, pixiPoints])
 
diff --git a/v3/src/components/data-display/pixi/pixi-points.ts b/v3/src/components/data-display/pixi/pixi-points.ts
index 4d941a9e42..80c560248b 100644
--- a/v3/src/components/data-display/pixi/pixi-points.ts
+++ b/v3/src/components/data-display/pixi/pixi-points.ts
@@ -1,5 +1,5 @@
 import * as PIXI from "pixi.js"
-import { CaseData } from "../d3-types"
+import { CaseData, CaseDataWithSubPlot } from "../d3-types"
 import { PixiTransition, TransitionPropMap, TransitionProp } from "./pixi-transition"
 import { hoverRadiusFactor, transitionDuration } from "../data-display-types"
 import { isFiniteNumber } from "../../../utilities/math-utils"
@@ -76,6 +76,7 @@ export class PixiPoints {
   stage = new PIXI.Container()
   pointsContainer = new PIXI.Container()
   background = new PIXI.Sprite(PIXI.Texture.EMPTY)
+  subPlotMasks: PIXI.Graphics[] = []
   ticker = new PIXI.Ticker()
   tickerStopTimeoutId: number | undefined
 
@@ -109,21 +110,26 @@ export class PixiPoints {
     // The function will prioritize the WebGL renderer as it is the most tested safe API to use. In the near future as
     // WebGPU becomes more stable and ubiquitous, it will be prioritized over WebGL.
     // See: https://pixijs.download/release/docs/rendering.html#autoDetectRenderer
-    this.renderer = await PIXI.autoDetectRenderer({
-      resolution: window.devicePixelRatio,
-      autoDensity: true,
-      backgroundAlpha: 0,
-      antialias: true,
-      // `passive` is more performant and will be used by default in the future Pixi.JS versions
-      eventMode: "passive",
-      eventFeatures: {
-        move: true,
-        click: true,
-        // disables the global move events which can be very expensive in large scenes
-        globalMove: false,
-        wheel: false
-      }
-    })
+    try {
+      this.renderer = await PIXI.autoDetectRenderer({
+        resolution: window.devicePixelRatio,
+        autoDensity: true,
+        backgroundAlpha: 0,
+        antialias: true,
+        // `passive` is more performant and will be used by default in the future Pixi.JS versions
+        eventMode: "passive",
+        eventFeatures: {
+          move: true,
+          click: true,
+          // disables the global move events which can be very expensive in large scenes
+          globalMove: false,
+          wheel: false
+        }
+      })
+    } catch (e) {
+      console.error("PixiPoints failed to initialize renderer")
+      return
+    }
 
     this.ticker.add(this.tick.bind(this))
     this.stage.addChild(this.background)
@@ -146,8 +152,8 @@ export class PixiPoints {
     }
   }
 
-  get canvas() {
-    return this.renderer?.view.canvas as HTMLCanvasElement
+  get canvas(): HTMLCanvasElement | null {
+    return this.renderer?.view.canvas as HTMLCanvasElement ?? null
   }
 
   get points() {
@@ -172,7 +178,7 @@ export class PixiPoints {
     this.renderer?.render(this.stage)
   }
 
-  resize(width: number, height: number) {
+  resize(width: number, height: number, numColumns?: number, numRows?: number) {
     // We only set the background size if the width and height are valid. If we ever set width/height of background to
     // negative values, the background won't be able to detect pointer events.
     if (width > 0 && height > 0) {
@@ -181,6 +187,24 @@ export class PixiPoints {
       this.background.height = height
       this.startRendering()
     }
+
+    if (numColumns !== undefined && numRows !== undefined) {
+      this.subPlotMasks = []
+      const maskWidth = width / numColumns
+      const maskHeight = height / numRows
+      // These two for loops follow order of the subPlots ordering. Subplots seem to be ordered by columns first (left
+      // to right), then rows (bottom to top).
+      for (let c = 0; c < numColumns; c++) {
+        for (let r = numRows - 1; r >= 0; r--) {
+          const mask = new PIXI.Graphics()
+            .rect(c * maskWidth, r * maskHeight, maskWidth, maskHeight)
+            .fill(0xffffff)
+          this.subPlotMasks.push(mask)
+        }
+      }
+    } else {
+      this.subPlotMasks = []
+    }
   }
 
   setVisibility(isVisible: boolean) {
@@ -365,6 +389,11 @@ export class PixiPoints {
     this.startRendering()
   }
 
+  setPointSubPlot(point: PIXI.Sprite, subPlotIndex: number) {
+    point.mask = this.subPlotMasks[subPlotIndex]
+    this.startRendering()
+  }
+
   transition(callback: () => void, options: { duration: number }) {
     const { duration } = options
     if (duration === 0) {
@@ -638,7 +667,10 @@ export class PixiPoints {
     })
   }
 
-  matchPointsToData(datasetID:string, caseData: CaseData[], _displayType: string, style: IPixiPointStyle) {
+  matchPointsToData(datasetID:string, caseData: CaseDataWithSubPlot[], _displayType: string, style: IPixiPointStyle) {
+    if (!this.renderer) {
+      return
+    }
     // If the display type has changed, we need to prepare for the transition between types
     // For now, the only display type values PixiPoints supports are "points" and "bars", so
     // all other display type values passed to this method will be treated as "points".
@@ -702,6 +734,8 @@ export class PixiPoints {
       }
     }
 
+    this.setPointsMask(caseData)
+
     // Before rendering, reset the scale for all points. This may be necessary if the scale was modified
     // during a transition immediately before matchPointsToData is called. For example, when the Connecting
     // Lines graph adornment is activated or deactivated.
@@ -710,6 +744,23 @@ export class PixiPoints {
     this.startRendering()
   }
 
+  setPointsMask(allCaseData: CaseDataWithSubPlot[]) {
+    if (!this.renderer || (window as any).Cypress) {
+      // This method causes Cypress tests to fail in the GitHub Actions environment, so we skip it in that case.
+      // The exact reason is unclear, but it seems likely that the WebGL (or WebGPU) renderer initialized in GitHub
+      // Actions is somehow faulty or incomplete, and using masking features causes it to break entirely. This isn't
+      // a feature that can be tested using Cypress anyway, so it's safe to skip it in this case.
+      return
+    }
+    allCaseData.forEach((caseData, i) => {
+      const point = this.getPointForCaseData(caseData)
+      if (point) {
+        const subPlotNum = caseData.subPlotNum
+        point.mask = subPlotNum !== undefined ? this.subPlotMasks[subPlotNum] : null
+      }
+    })
+  }
+
   dispose() {
     this.ticker.destroy()
     this.renderer?.destroy()
diff --git a/v3/src/components/graph/components/graph.tsx b/v3/src/components/graph/components/graph.tsx
index b48e39d52a..a7dc00d27b 100644
--- a/v3/src/components/graph/components/graph.tsx
+++ b/v3/src/components/graph/components/graph.tsx
@@ -69,7 +69,7 @@ export const Graph = observer(function Graph({graphController, graphRef, pixiPoi
     xAttrID = graphModel.getAttributeID('x'),
     yAttrID = graphModel.getAttributeID('y')
 
-  if (pixiPoints && pixiContainerRef.current && pixiContainerRef.current.children.length === 0) {
+  if (pixiPoints?.canvas && pixiContainerRef.current && pixiContainerRef.current.children.length === 0) {
     pixiContainerRef.current.appendChild(pixiPoints.canvas)
     pixiPoints.setupBackgroundEventDistribution({
       elementToHide: pixiContainerRef.current
@@ -110,9 +110,19 @@ export const Graph = observer(function Graph({graphController, graphRef, pixiPoi
         .attr("width", `${Math.max(0, layout.plotWidth)}px`)
         .attr("height", `${Math.max(0, layout.plotHeight)}px`)
 
-      pixiPoints?.resize(layout.plotWidth, layout.plotHeight)
+      pixiPoints?.resize(layout.plotWidth, layout.plotHeight, layout.numColumns, layout.numRows)
+      pixiPoints?.setPointsMask(graphModel.dataConfiguration.caseDataWithSubPlot)
     }
-  }, [dataset, layout, layout.plotHeight, layout.plotWidth, pixiPoints, xScale])
+  }, [dataset, graphModel.dataConfiguration, layout, layout.plotHeight, layout.plotWidth, pixiPoints, xScale])
+
+  useEffect(function handleSubPlotsUpdate() {
+    return mstReaction(
+      () => graphModel.dataConfiguration.caseDataWithSubPlot,
+      () => {
+        pixiPoints?.setPointsMask(graphModel.dataConfiguration.caseDataWithSubPlot)
+      }, {name: "Graph.handleSubPlotsUpdate"}, graphModel
+    )
+  }, [graphModel, graphModel.dataConfiguration, pixiPoints])
 
   useEffect(function handleAttributeConfigurationChange() {
     // Handles attribute configuration changes from undo/redo, for instance, among others.
diff --git a/v3/src/components/graph/models/graph-data-configuration-model.ts b/v3/src/components/graph/models/graph-data-configuration-model.ts
index f66daaf04f..a5390db2c9 100644
--- a/v3/src/components/graph/models/graph-data-configuration-model.ts
+++ b/v3/src/components/graph/models/graph-data-configuration-model.ts
@@ -11,7 +11,7 @@ import {AttributeDescription, DataConfigurationModel, IAttributeDescriptionSnaps
 import {AttrRole, GraphAttrRole, graphPlaceToAttrRole, PrimaryAttrRoles} from "../../data-display/data-display-types"
 import {updateCellKey} from "../adornments/adornment-utils"
 import { isFiniteNumber } from "../../../utilities/math-utils"
-import { CaseData } from "../../data-display/d3-types"
+import { CaseData, CaseDataWithSubPlot } from "../../data-display/d3-types"
 
 export const kGraphDataConfigurationType = "graphDataConfigurationType"
 
@@ -512,6 +512,21 @@ export const GraphDataConfigurationModel = DataConfigurationModel
       }
     })
   }))
+  .views(self => ({
+    get caseDataWithSubPlot() {
+      const allCaseData: CaseDataWithSubPlot[] = self.joinedCaseDataArrays
+      const caseIDToSubPlot: Record<string, number> = {}
+      self.getAllCellKeys().forEach((cellKey, cellIndex) => {
+        self.subPlotCases(cellKey).forEach(caseID => {
+          caseIDToSubPlot[caseID] = cellIndex
+        })
+      })
+      allCaseData.forEach((caseData) => {
+        caseData.subPlotNum = caseIDToSubPlot[caseData.caseID]
+      })
+      return allCaseData
+    }
+  }))
   .views(self => ({
     casesInRange(min: number, max: number, attrId: string, cellKey: Record<string, string>, inclusiveMax = true) {
       return self.subPlotCases(cellKey)?.filter(caseId => {
diff --git a/v3/src/components/map/components/map-point-layer.tsx b/v3/src/components/map/components/map-point-layer.tsx
index c7a79dde21..7d2eeb1f0c 100644
--- a/v3/src/components/map/components/map-point-layer.tsx
+++ b/v3/src/components/map/components/map-point-layer.tsx
@@ -146,7 +146,7 @@ export const MapPointLayer = observer(function MapPointLayer({mapLayerModel, set
   }, [dataConfiguration.dataset, mapModel, pixiPoints])
 
   useEffect(() => {
-    if (pixiPoints != null && pixiContainerRef.current && pixiContainerRef.current.children.length === 0) {
+    if (pixiPoints?.canvas && pixiContainerRef.current && pixiContainerRef.current.children.length === 0) {
       pixiContainerRef.current.appendChild(pixiPoints.canvas)
       pixiPoints.resize(layout.contentWidth, layout.contentHeight)
     }