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...

Cell[]	GetCells (int group)
	Returns cell that belong to a certain selection group. More...

Cell[]	GetCells (int group, Cell[] subSelection)
	Returns cell that belong to a certain selection group within a certain sub selection of cells. More...

int	GetNumberOfCells ()

void	HighlightCells (Cell[] cellsToHighlight, bool highlight)

void	HighlightAttribute (string attribute)
	Highlights an attribute in all graphs. More...

void	HighlightGroup (Selection selection, int group)
	Highlights a group from a selection in all graphs. More...

void	ResetHighlight ()
	Resets any highlighting in all graphs. 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, int colIndex=0)
	Color all cells that belong to a certain attribute. More...

void	ColorAllClusters (float[] cellClusters, bool color)
	Used by ScarfManager. Adds or removes cells to the current selection. More...

void	ColorByGene (float[] values)
	Used be ScarfManager. Colors the graphs based off the colors in values . Indices are cellnames 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...

IEnumerable< string >	GetAttributes (string cellname)
	Get all attributes that a cell belongs to. More...

IEnumerable< string >	GetAttributes (Cell cell)
	Get all attributes that a cell belongs to. More...

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

void	ColorClusters (string path)

void	ColorByNumericalAttribute (string name)

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

Public Attributes
ReferenceManager	referenceManager

Dictionary< string, GameObject >	convexHulls = new Dictionary<string, GameObject>()

List< string >	cellNames = new List<string>()

Properties
List< string >	AttributesNames `[get, set]`

Dictionary< string, HashSet< Cell > >	Attributes `[get, set]`

string[]	Facs `[get, set]`

string[]	Facs_values `[get, set]`

string[]	NumericalAttributes `[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...

Dictionary< string, Tuple< float, float > >	NumericalAttributeRanges `[get]`

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.

◆ ColorAllClusters()

void CellexalVR.AnalysisLogic.CellManager.ColorAllClusters	(	float[]	cellClusters,
		bool	color
	)

Used by ScarfManager. Adds or removes cells to the current selection.

Parameters

cellClusters	An array mapping a cellname (index) to a cluster.
color	True if the cells in cellClusters should be added to the current the selection, false if they should be removed."/>

◆ ColorByAttribute()

void CellexalVR.AnalysisLogic.CellManager.ColorByAttribute	(	string	attributeType,
		bool	color,
		bool	subGraph = `false`,
		int	colIndex = `0`
	)

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.

◆ ColorByGene()

void CellexalVR.AnalysisLogic.CellManager.ColorByGene ( float[] values )

Used be ScarfManager. Colors the graphs based off the colors in values . Indices are cellnames

Parameters

values An array of floats mapping cellnames (indices) to an expression value.

◆ 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.

◆ GetAttributes() [1/2]

IEnumerable<string> CellexalVR.AnalysisLogic.CellManager.GetAttributes ( Cell cell )

Get all attributes that a cell belongs to.

Parameters

cell	The cell to get attributes for.

Returns: An IEnumerable<string> containing all attributes the cell belongs to.

◆ GetAttributes() [2/2]

IEnumerable<string> CellexalVR.AnalysisLogic.CellManager.GetAttributes ( string cellname )

Get all attributes that a cell belongs to.

Parameters

cellname The cell to get attributes for.

Returns: An IEnumerable<string> containing all attributes the cell belongs to.

◆ GetCell()

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

Finds cell and returns it.

Parameters

label The label(id) of the cell.

Returns

◆ GetCells() [1/3]

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

Returns all cells.

Returns

◆ GetCells() [2/3]

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

Returns cell that belong to a certain selection group.

Parameters

group

Returns

◆ GetCells() [3/3]

Cell [] CellexalVR.AnalysisLogic.CellManager.GetCells	(	int	group,
		Cell[]	subSelection
	)

Returns cell that belong to a certain selection group within a certain sub selection of cells.

Parameters

group	The cells beloning to this particular group will be returned.
subSelection	The subselection of cells to select from.

Returns

◆ HighlightAttribute()

void CellexalVR.AnalysisLogic.CellManager.HighlightAttribute ( string attribute )

Highlights an attribute in all graphs.

Parameters

attribute The attribute to highlight

◆ HighlightGroup()

void CellexalVR.AnalysisLogic.CellManager.HighlightGroup	(	Selection	selection,
		int	group
	)

Highlights a group from a selection in all graphs.

Parameters

selection	The selection to color by.
group	The group to color by.

◆ 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

◆ ResetHighlight()

void CellexalVR.AnalysisLogic.CellManager.ResetHighlight ( )

Resets any highlighting in all graphs.

◆ 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:

cellexalvr_cloudxr/Assets/Scripts/AnalysisLogic/CellManager.cs

Public Member Functions

Public Attributes

Properties

Detailed Description

Member Function Documentation

◆ AddAttribute()

◆ AddCell()

◆ AddToPrunedGenes()

◆ ColorAllClusters()

◆ ColorByAttribute()

◆ ColorByAttributeExpression()

◆ ColorByGene()

◆ ColorByIndex()

◆ ColorGraphsByGene() [1/2]

◆ ColorGraphsByGene() [2/2]

◆ CreateNewSelection()

◆ DeleteCells()

◆ GetAttributes() [1/2]

◆ GetAttributes() [2/2]

◆ GetCell()

◆ GetCells() [1/3]

◆ GetCells() [2/3]

◆ GetCells() [3/3]

◆ HighlightAttribute()

◆ HighlightGroup()

◆ QueryTopGenes()

◆ ResetHighlight()

◆ SendToSelection()

◆ SubSet()

Property Documentation

◆ FacsRanges