This class represent a manager that holds all the cells. More...

Inheritance diagram for CellexalVR.AnalysisLogic.CellManager:

Public Member Functions
Cell	AddCell (string label)
	Attempts to add a cell to the dictionary More...

Cell	GetCell (string label)
	Finds cell and returns it. More...

Cell[]	GetCells ()
	Returns all cells. More...

void	CreateNewSelection (string graphName, string[] cellnames, int[] groups, Dictionary< int, Color > groupingColors=null)
	Creates a new selection. More...

void	ColorGraphsByGene (string geneName)

void	ColorGraphsByGene (string geneName, bool triggerEvent=true)
	Colors all GraphPoints in all current Graphs based on their expression of a gene. More...

void	ColorGraphsByGene (string geneName, GraphManager.GeneExpressionColoringMethods coloringMethod, bool triggerEvent=true)
	Colors all GraphPoints in all current Graphs based on their expression of a gene. More...

void	QueryTopGenes (SQLite.QueryTopGenesRankingMode mode)
	Queries the database for all genes and sorts them based on the chosen mode. More...

void	AddToPrunedGenes (string[] genesToAdd)
	Used by the database to tell the cellmanager which genes were actually in the database. More...

void	DeleteCells ()
	Removes all cells. More...

void	ColorByAttribute (string attributeType, bool color, bool subGraph=false)
	Color all cells that belong to a certain attribute. More...

void	SendToSelection ()
	Adds the currently selected attributes as a selection. More...

void	ColorByAttributeExpression (BooleanExpression.Expr expr)
	Color all cells based on an expression of attributes More...

void	AddAttribute (string cellname, string attributeType, int group)
	Adds an attribute to a cell. More...

void	ColorByIndex (string name)
	Color all graphpoints according to a column in the index.facs file. More...

IEnumerator	DrawLinesBetweenGraphPoints (List< Graph.GraphPoint > points)
	Draws lines between the graph that was selected from to points in other graphs that share the same cell label. More...

void	ClearLinesBetweenGraphPoints ()
	Removes all lines between graphs. More...

List< Cell >	SubSet (BooleanExpression.Expr expr)
	Returns a subset of all cells in the dataset based on a boolean expression. More...

Public Attributes
GameObject	clusterDebugBox

ReferenceManager	referenceManager

GameObject	lineBetweenTwoGraphPointsPrefab

GameObject	pointClusterPrefab

Properties
string[]	Attributes `[get, set]`

string[]	Facs `[get, set]`

string[]	Facs_values `[get, set]`

float	LowestExpression `[get]`

float	HighestExpression `[get]`

Dictionary< string, Tuple< float, float > >	FacsRanges `[get]`
	Lowest and highest range of facs measurements. Tuple<T1, T2>.Item1 is the lowest value and Tuple<T1, T2>.Item2 is the highest. More...

Detailed Description

This class represent a manager that holds all the cells.

Member Function Documentation

◆ AddAttribute()

void CellexalVR.AnalysisLogic.CellManager.AddAttribute	(	string	cellname,
		string	attributeType,
		int	group
	)

Adds an attribute to a cell.

Parameters

cellname	The cells name.
attributeType	The attribute type / name
group	The attribute value

◆ AddCell()

Cell CellexalVR.AnalysisLogic.CellManager.AddCell ( string label )

Attempts to add a cell to the dictionary

Parameters

label The cell's name

Returns: Returns a reference to the added cell

◆ AddToPrunedGenes()

void CellexalVR.AnalysisLogic.CellManager.AddToPrunedGenes ( string[] genesToAdd )

Used by the database to tell the cellmanager which genes were actually in the database.

Parameters

genesToAdd An array of genes that was in the database.

◆ ClearLinesBetweenGraphPoints()

void CellexalVR.AnalysisLogic.CellManager.ClearLinesBetweenGraphPoints ( )

Removes all lines between graphs.

◆ ColorByAttribute()

void CellexalVR.AnalysisLogic.CellManager.ColorByAttribute	(	string	attributeType,
		bool	color,
		bool	subGraph = `false`
	)

Color all cells that belong to a certain attribute.

Parameters

attributeType	The name of the attribute.
color	True if the graphpoints should be colored to the attribute's color, false if they should be white.

◆ ColorByAttributeExpression()

void CellexalVR.AnalysisLogic.CellManager.ColorByAttributeExpression ( BooleanExpression.Expr expr )

Color all cells based on an expression of attributes

Parameters

expr	The root of the tree representing a boolean expression of attributes.

◆ ColorByIndex()

void CellexalVR.AnalysisLogic.CellManager.ColorByIndex ( string name )

Color all graphpoints according to a column in the index.facs file.

◆ ColorGraphsByGene() [1/2]

void CellexalVR.AnalysisLogic.CellManager.ColorGraphsByGene	(	string	geneName,
		bool	triggerEvent = `true`
	)

Colors all GraphPoints in all current Graphs based on their expression of a gene.

Parameters

geneName The name of the gene.

◆ ColorGraphsByGene() [2/2]

void CellexalVR.AnalysisLogic.CellManager.ColorGraphsByGene	(	string	geneName,
		GraphManager.GeneExpressionColoringMethods	coloringMethod,
		bool	triggerEvent = `true`
	)

Colors all GraphPoints in all current Graphs based on their expression of a gene.

Parameters

geneName The name of the gene.

◆ CreateNewSelection()

void CellexalVR.AnalysisLogic.CellManager.CreateNewSelection	(	string	graphName,
		string[]	cellnames,
		int[]	groups,
		Dictionary< int, Color >	groupingColors = `null`
	)

Creates a new selection.

Parameters

graphName	The graph that the selection originated from.
cellnames	An array of all the cell names (the graphpoint labels).
groups	An array of all colors that the cells should have.
groupingColors	Optional parameter, used if a custom color scheme should be used. Maps groups to colors.

◆ DeleteCells()

void CellexalVR.AnalysisLogic.CellManager.DeleteCells ( )

Removes all cells.

◆ DrawLinesBetweenGraphPoints()

IEnumerator CellexalVR.AnalysisLogic.CellManager.DrawLinesBetweenGraphPoints ( List< Graph.GraphPoint > points )

Draws lines between the graph that was selected from to points in other graphs that share the same cell label.

Parameters

points The graphpoints to draw the lines from.

◆ GetCell()

Cell CellexalVR.AnalysisLogic.CellManager.GetCell ( string label )

Finds cell and returns it.

Parameters

label The label(id) of the cell.

Returns

◆ GetCells()

Cell [] CellexalVR.AnalysisLogic.CellManager.GetCells ( )

Returns all cells.

Returns

◆ QueryTopGenes()

void CellexalVR.AnalysisLogic.CellManager.QueryTopGenes ( SQLite.QueryTopGenesRankingMode mode )

Queries the database for all genes and sorts them based on the chosen mode.

Parameters

mode	The chosen mode. SQLite.QueryTopGenesRankingMode

◆ SendToSelection()

void CellexalVR.AnalysisLogic.CellManager.SendToSelection ( )

Adds the currently selected attributes as a selection.

◆ SubSet()

List<Cell> CellexalVR.AnalysisLogic.CellManager.SubSet ( BooleanExpression.Expr expr )

Returns a subset of all cells in the dataset based on a boolean expression.

Property Documentation

◆ FacsRanges

Dictionary<string, Tuple<float, float> > CellexalVR.AnalysisLogic.CellManager.FacsRanges

get

Lowest and highest range of facs measurements. Tuple<T1, T2>.Item1 is the lowest value and Tuple<T1, T2>.Item2 is the highest.

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

Assets/Scripts/AnalysisLogic/CellManager.cs

Public Member Functions

Public Attributes

Properties

Detailed Description

Member Function Documentation

◆ AddAttribute()

◆ AddCell()

◆ AddToPrunedGenes()

◆ ClearLinesBetweenGraphPoints()

◆ ColorByAttribute()

◆ ColorByAttributeExpression()

◆ ColorByIndex()

◆ ColorGraphsByGene() [1/2]

◆ ColorGraphsByGene() [2/2]

◆ CreateNewSelection()

◆ DeleteCells()

◆ DrawLinesBetweenGraphPoints()

◆ GetCell()

◆ GetCells()

◆ QueryTopGenes()

◆ SendToSelection()

◆ SubSet()

Property Documentation

◆ FacsRanges