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

Inheritance diagram for CellexalVR.AnalysisObjects.Graph:

Classes
struct	ColorByMaskJob

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

struct	HighlightMaskMultiJob

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

struct	ResetHighlightMaskMultiJob

struct	SetChannelsJob

Public Member Functions
void	MakeAllPointsCullable (bool toggle)
	Sets green channel of points so culling will be activated in the shader. This means that inside the culling cube the points will not be visible. More...

void	DeleteGraph (string tag)
	Used to delete a graph. Starts the minimizing animation and then deletes the object. More...

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

async void	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	ToggleInfoText ()
	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 ()
	Moves this graph back to its original location. More...

void	ResetSizeAndRotation ()
	Resets this graph's scale and rotation back to its original values. More...

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

void	ColorBySelection (Selection selection)
	Colors this graph by a selection. GraphPoints that are not in this selection are not changed. More...

void	ColorSelectionGroup (Selection selection, int group)
	Colors this graph by one group of a selection. More...

void	HighlightAttribute (string attribute)
	Highlights, all graphpoints that belong to an attribute. More...

void	HighlightSelectionGroup (Selection selection, int group)
	Highlights a group from a Selection. More...

void	ResetHighlight ()
	Resets all highlighted graphpoints, retaining their colour but un-highlighting them. More...

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

Color	GetGraphPointColor (GraphPoint point)
	Gets the color of a graph point. More...

void	Party ()

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

void	ColorGraphPointGeneExpression (GraphPoint graphPoint, int i)
	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	ColorGraphPointsSelectionColor (IEnumerable< GraphPoint > points, int i, bool outline)
	Colors a collection of graphpoints by one of the selection colors. More...

void	MakeAllPointsTransparent (bool toggle)
	Sets the green channel of the point so transparency will be activated in the shader. More...

void	MakePointUnCullable (GraphPoint graphPoint, bool culling)
	Sets blue channel of point so culling will be deactivated in the shader. This means that inside the culling cube the poins will still be visible. 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...

void	ColorByAttribute (string attribute, bool color)
	Color, or un-color, all graphpoints that belong to an attribute. More...

void	CopyAttributeMasks (Graph graph)
	Copies the attribute mask data from another graph and reformats it to this graph's meshs' clustering. 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...

List< GraphPoint >	MinkowskiDetection (Vector3 sphereCenter, float radius, int group=-1)
	Finds all GraphPoint that are inside a sphere. More...

Public Attributes
GameObject	skeletonPrefab

GameObject	emptySkeletonPrefab

Material	lineMaterial

GameObject	movingOutlineCircle

GameObject	convexHull

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

GraphManager	graphManager

GameObject	infoParent

TextMeshPro	graphNameText

TextMeshPro	graphInfoText

TextMeshPro	graphNrText

LegendManager	legendManager

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>()

ReferenceManager	referenceManager

int	lodGroups

bool	scaled

Dictionary< int, List< GameObject > >	lodGroupClusters = new Dictionary<int, List<GameObject>>()

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

int	textureWidth

int	textureHeight

Texture2D	texture

Dictionary< string, Texture2D >	attributeMasks = new Dictionary<string, Texture2D>()

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
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.

◆ ColorByAttribute()

void CellexalVR.AnalysisObjects.Graph.ColorByAttribute	(	string	attribute,
		bool	color
	)

Color, or un-color, all graphpoints that belong to an attribute.

Parameters

attribute	The name of the attribute, should be in the full format e.g. "<c>type@attribute</c>".
color	True if graphpoints belonging should be colored, false if un-coloring.

◆ 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.

◆ ColorBySelection()

void CellexalVR.AnalysisObjects.Graph.ColorBySelection ( Selection selection )

Colors this graph by a selection. GraphPoints that are not in this selection are not changed.

Parameters

selection The selection to color by.

◆ ColorGraphPointGeneExpression()

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

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.

◆ ColorGraphPointsSelectionColor()

void CellexalVR.AnalysisObjects.Graph.ColorGraphPointsSelectionColor	(	IEnumerable< GraphPoint >	points,
		int	i,
		bool	outline
	)

Colors a collection of graphpoints by one of the selection colors.

Parameters

points	The points 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.

◆ ColorSelectionGroup()

void CellexalVR.AnalysisObjects.Graph.ColorSelectionGroup	(	Selection	selection,
		int	group
	)

Colors this graph by one group of a selection.

Parameters

selection	The selection containing the group to color by.
group	The group's id, as defined by Selection.groups.

◆ CopyAttributeMasks()

void CellexalVR.AnalysisObjects.Graph.CopyAttributeMasks ( Graph graph )

Copies the attribute mask data from another graph and reformats it to this graph's meshs' clustering.

Parameters

graph The graph to coopy from.

◆ CreateGraphSkeleton()

async void 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.

◆ DeleteGraph()

void CellexalVR.AnalysisObjects.Graph.DeleteGraph ( string tag )

Used to delete a graph. Starts the minimizing animation and then deletes the object.

Parameters

tag

◆ 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.

◆ GetGraphPointColor()

Color CellexalVR.AnalysisObjects.Graph.GetGraphPointColor ( GraphPoint point )

Gets the color of a graph point.

Parameters

point The graph point.

Returns: The color from GraphGenerator.graphPointColors that the point is currently using.

◆ HighlightAttribute()

void CellexalVR.AnalysisObjects.Graph.HighlightAttribute ( string attribute )

Highlights, all graphpoints that belong to an attribute.

Parameters

attribute The name of the attribute, should be in the full format "<c>type@attribute</c>".

◆ HighlightSelectionGroup()

void CellexalVR.AnalysisObjects.Graph.HighlightSelectionGroup	(	Selection	selection,
		int	group
	)

Highlights a group from a Selection.

Parameters

selection	The selection containing the group.
group	The group's number, as defined in Selection.groups.

◆ MakeAllPointsCullable()

void CellexalVR.AnalysisObjects.Graph.MakeAllPointsCullable ( bool toggle )

Sets green channel of points so culling will be activated in the shader. This means that inside the culling cube the points will not be visible.

Parameters

toggle

◆ MakeAllPointsTransparent()

void CellexalVR.AnalysisObjects.Graph.MakeAllPointsTransparent ( bool toggle )

Sets the green channel of the point so transparency will be activated in the shader.

Parameters

toggle True to make points transparent, false to make points opaque.

◆ MakePointUnCullable()

void CellexalVR.AnalysisObjects.Graph.MakePointUnCullable	(	GraphPoint	graphPoint,
		bool	culling
	)

Sets blue channel of point so culling will be deactivated in the shader. This means that inside the culling cube the poins will still be visible.

◆ MinkowskiDetection() [1/2]

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.

◆ MinkowskiDetection() [2/2]

List<GraphPoint> CellexalVR.AnalysisObjects.Graph.MinkowskiDetection	(	Vector3	sphereCenter,
		float	radius,
		int	group = `-1`
	)

Finds all GraphPoint that are inside a sphere.

Parameters

sphereCenter	The sphere's center, in local coordinates.
radius	The sphere's radius.
group	The group to assign the found points. Points already in this group will be ignored, unless -1 is passed as this argument.

Returns: A list of all GraphPoint that are inside the sphere.

◆ ResetColors()

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

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

◆ ResetHighlight()

void CellexalVR.AnalysisObjects.Graph.ResetHighlight ( )

Resets all highlighted graphpoints, retaining their colour but un-highlighting them.

◆ ResetPosition()

void CellexalVR.AnalysisObjects.Graph.ResetPosition ( )

Moves this graph back to its original location.

◆ ResetSizeAndRotation()

void CellexalVR.AnalysisObjects.Graph.ResetSizeAndRotation ( )

Resets this graph's scale and rotation back to its original values.

◆ 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.

Summertweriking

◆ 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.

◆ ToggleGraphPoints()

void CellexalVR.AnalysisObjects.Graph.ToggleGraphPoints ( )

Toggles all graphpoint cluster gameobjects active/inactive.

◆ ToggleInfoText()

void CellexalVR.AnalysisObjects.Graph.ToggleInfoText ( )

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

Parameters

visible True for visible, false for invisible

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

cellexalvr_cloudxr/Assets/Scripts/AnalysisObjects/Graph.cs

Classes

Public Member Functions

Public Attributes

Properties

Detailed Description

Member Function Documentation

◆ ClearTopExprCircles()

◆ ColorByAttribute()

◆ ColorByGeneExpression()

◆ ColorBySelection()

◆ ColorGraphPointGeneExpression()

◆ ColorGraphPointSelectionColor()

◆ ColorGraphPointsSelectionColor()

◆ ColorSelectionGroup()

◆ CopyAttributeMasks()

◆ CreateGraphSkeleton()

◆ DeleteGraph()

◆ FindGraphPoint()

◆ GetGraphPointColor()

◆ HighlightAttribute()

◆ HighlightSelectionGroup()

◆ MakeAllPointsCullable()

◆ MakeAllPointsTransparent()

◆ MakePointUnCullable()

◆ MinkowskiDetection() [1/2]

◆ MinkowskiDetection() [2/2]

◆ ResetColors()

◆ ResetHighlight()

◆ ResetPosition()

◆ ResetSizeAndRotation()

◆ ScaleCoordinates()

◆ SetAxesVisible()

◆ SetInfoText()

◆ ToggleGraphPoints()

◆ ToggleInfoText()