Represents a graph consisting of multiple GraphPoints. More...

Inheritance diagram for CellexalVR.AnalysisObjects.Graph:

Classes
class	GraphPoint
	A graph point represents a point in the graphs as well as one cell in the dimension reduced data. More...

class	OctreeNode
	Private class to represent one node in the octree used for collision detection More...

Public Member Functions
Vector3	ScaleCoordinates (Vector3 coords)
	Scales one Vector3 of coordinates from the original scale to the graph's desired scale. More...

void	OnDrawGizmos ()

IEnumerator	CreateGraphSkeleton (bool empty=false)
	Method to greate lines between nodes in the octree. This gives a sort of skeleton representation of the graph. More...

void	SetInfoText ()
	Tells this graph that all graphpoints are added to this graph and we can update the info text. More...

void	SetInfoTextVisible (bool visible)
	Set this graph's info panel visible or not visible. More...

void	SetAxesVisible (bool visible)
	Set this graph's axes visible or not visible. More...

void	ResetPosition ()

void	ResetSizeAndRotation ()

void	ResetColors (bool resetGroup=true)
	Resets the color of all graphpoints in this graph to white. More...

void	ToggleGraphPoints ()
	Toggles all graphpoint cluster gameobjects active/inactive. More...

Color	GetGraphPointColor (GraphPoint gp)

void	Party ()

void	ClearTopExprCircles ()
	Clears the circles from previous colouring so it doesn't stack. More...

void	ColorGraphPointGeneExpression (GraphPoint graphPoint, int i, bool outline)
	Recolors a single graphpoint. More...

void	ColorGraphPointSelectionColor (GraphPoint graphPoint, int i, bool outline)
	Colors one graph point based on one of the selection colors. More...

void	HighlightGraphPoint (GraphPoint graphPoint, bool active)

void	ResetGraphPointColor (GraphPoint graphPoint)
	Resets the color of the graph point back to its default. More...

GraphPoint	FindGraphPoint (string label)
	Finds a graph point by its name. More...

void	ColorByGeneExpression (ArrayList expressions)
	Color all graphpoints in this graph with the expression of some gene. More...

List< GraphPoint >	MinkowskiDetection (Vector3 selectionToolPos, Vector3 selectionToolBoundsCenter, Vector3 selectionToolBoundsExtents, int group)
	Finds all GraphPoint that are inside the selection tool. This is done by traversing the generated Octree and dismissing subtrees using Minkowski differences. Ultimately, raycasting is used to find collisions because the selection tool is not a box. More...

Public Attributes
GameObject	skeletonPrefab

GameObject	emptySkeletonPrefab

Material	skeletonMaterial

Material	lineMaterial

GameObject	movingOutlineCircle

GameObject	convexHull

GraphManager	graphManager

TextMeshPro	graphNameText

TextMeshPro	graphInfoText

TextMeshPro	graphNrText

GameObject	axes

GameObject	annotationsParent

string[]	axisNames = new string[3]

bool	GraphActive = true

Dictionary< string, GraphPoint >	points = new Dictionary<string, GraphPoint>()

Dictionary< string, GraphPoint >	subSelectionPoints = new Dictionary<string, GraphPoint>()

List< Vector3 >	pointsPositions

ReferenceManager	referenceManager

List< GameObject >	graphPointClusters = new List<GameObject>()

int	textureWidth

int	textureHeight

Texture2D	texture

Vector3	minCoordValues = new Vector3(float.MaxValue, float.MaxValue, float.MaxValue)

Vector3	maxCoordValues = new Vector3(float.MinValue, float.MinValue, float.MinValue)

List< GameObject >	topExprCircles = new List<GameObject>()

Vector3	diffCoordValues

float	longestAxis

Vector3	scaledOffset

int	nbrOfClusters

VelocityParticleEmitter	velocityParticleEmitter

GameObject	lineParent

bool	hasVelocityInfo

bool	graphPointsInactive = false

OctreeNode	octreeRoot

Properties
List< GameObject >	CTCGraphs `[get, set]`

string	GraphName `[get, set]`

string	FolderName `[get, set]`

int	GraphNumber `[get, set]`

Detailed Description

Represents a graph consisting of multiple GraphPoints.

Member Function Documentation

◆ ClearTopExprCircles()

void CellexalVR.AnalysisObjects.Graph.ClearTopExprCircles ( )

Clears the circles from previous colouring so it doesn't stack.

◆ ColorByGeneExpression()

void CellexalVR.AnalysisObjects.Graph.ColorByGeneExpression ( ArrayList expressions )

Color all graphpoints in this graph with the expression of some gene.

Parameters

expressions An arraylist with CellExpressionPair.

◆ ColorGraphPointGeneExpression()

void CellexalVR.AnalysisObjects.Graph.ColorGraphPointGeneExpression	(	GraphPoint	graphPoint,
		int	i,
		bool	outline
	)

Recolors a single graphpoint.

Parameters

graphPoint	The graphpoint to recolor.
color	The graphpoint's new color.

◆ ColorGraphPointSelectionColor()

void CellexalVR.AnalysisObjects.Graph.ColorGraphPointSelectionColor	(	GraphPoint	graphPoint,
		int	i,
		bool	outline
	)

Colors one graph point based on one of the selection colors.

Parameters

graphPoint	The graph point to color.
i	An integer betweeen 0 and the number of selection colors.
outline	True if the graph point should get an outline as well, false otherwise.

◆ CreateGraphSkeleton()

IEnumerator CellexalVR.AnalysisObjects.Graph.CreateGraphSkeleton ( bool empty = false )

Method to greate lines between nodes in the octree. This gives a sort of skeleton representation of the graph.

◆ FindGraphPoint()

GraphPoint CellexalVR.AnalysisObjects.Graph.FindGraphPoint ( string label )

Finds a graph point by its name.

Parameters

label The name of the graph point

Returns: The graph point, or null if was not found.

◆ MinkowskiDetection()

List<GraphPoint> CellexalVR.AnalysisObjects.Graph.MinkowskiDetection	(	Vector3	selectionToolPos,
		Vector3	selectionToolBoundsCenter,
		Vector3	selectionToolBoundsExtents,
		int	group
	)

Finds all GraphPoint that are inside the selection tool. This is done by traversing the generated Octree and dismissing subtrees using Minkowski differences. Ultimately, raycasting is used to find collisions because the selection tool is not a box.

Parameters

selectionToolPos	The selection tool's position in world space.
selectionToolBoundsCenter	The selection tool's bounding box's center in world space.
selectionToolBoundsExtents	The selection tool's bounding box's extents in world space.
group	The group that the selection tool is set to color the graphpoints by.

Returns: A List<CombinedGraphPoint> with all GraphPoint that are inside the selecion tool.

◆ ResetColors()

void CellexalVR.AnalysisObjects.Graph.ResetColors ( bool resetGroup = true )

Resets the color of all graphpoints in this graph to white.

◆ ResetGraphPointColor()

void CellexalVR.AnalysisObjects.Graph.ResetGraphPointColor ( GraphPoint graphPoint )

Resets the color of the graph point back to its default.

Parameters

graphPoint The graphpoint to recolor.

◆ ScaleCoordinates()

Vector3 CellexalVR.AnalysisObjects.Graph.ScaleCoordinates ( Vector3 coords )

Scales one Vector3 of coordinates from the original scale to the graph's desired scale.

Parameters

coords The coordinates to scale.

Returns: A scaled Vector3.

◆ SetAxesVisible()

void CellexalVR.AnalysisObjects.Graph.SetAxesVisible ( bool visible )

Set this graph's axes visible or not visible.

Parameters

visible True for visible, false for invisible

◆ SetInfoText()

void CellexalVR.AnalysisObjects.Graph.SetInfoText ( )

Tells this graph that all graphpoints are added to this graph and we can update the info text.

◆ SetInfoTextVisible()

void CellexalVR.AnalysisObjects.Graph.SetInfoTextVisible ( bool visible )

Set this graph's info panel visible or not visible.

Parameters

visible True for visible, false for invisible

◆ ToggleGraphPoints()

void CellexalVR.AnalysisObjects.Graph.ToggleGraphPoints ( )

Toggles all graphpoint cluster gameobjects active/inactive.

The documentation for this class was generated from the following file:

Assets/Scripts/AnalysisObjects/Graph.cs

Classes

Public Member Functions

Public Attributes

Properties

Detailed Description

Member Function Documentation

◆ ClearTopExprCircles()

◆ ColorByGeneExpression()

◆ ColorGraphPointGeneExpression()

◆ ColorGraphPointSelectionColor()

◆ CreateGraphSkeleton()

◆ FindGraphPoint()

◆ MinkowskiDetection()

◆ ResetColors()

◆ ResetGraphPointColor()

◆ ScaleCoordinates()

◆ SetAxesVisible()

◆ SetInfoText()

◆ SetInfoTextVisible()

◆ ToggleGraphPoints()