CellexalVR.AnalysisLogic.HeatmapGenerator Class Reference

A generator for heatmaps. More...

Inheritance diagram for CellexalVR.AnalysisLogic.HeatmapGenerator:

Public Member Functions
void	LoadHeatmap (string heatmapName, string fromSelectionFile="")
void	InitColors ()
	Initializes expressionColors with the colors in the config file. More...
void	CreateHeatmap ()
void	CreateHeatmap (string heatmapName="")
	Creates a new heatmap using the last confirmed selection. More...
void	DeleteHeatmap (string heatmapName)
	Removes one heatmap. More...
Heatmap	FindHeatmap (string heatmapName)
	Finds a heatmap. More...
void	HighLightGene (string geneName)
	Highlights gene in genelist in all the heatmaps if it is there. More...
void	BuildTexture (Selection selection, string filepath, Heatmap heatmap, bool newHeatmap=true)
	Builds the heatmap texture. More...
void	BuildTexture (Heatmap heatmap, bool newHeatmap=true)
	Builds a heatmap texture based on already known groupwidths and attribute widths. More...
void	BuildTexture (Cell[] newCells, string[] newGenes, List< Tuple< int, float, int >> newGroupWidths, Heatmap heatmap)
	Builds this heatmaps texture using the supplied cells and genes. More...
IEnumerator	BuildTextureCoroutine (Heatmap heatmap, bool newHeatmap=true)
	Coroutine that starts a thread and generates the heatmap. More...
void	CreateHeatmapPNG (Heatmap heatmap, ArrayList result, Dictionary< string, int > genePositions, Dictionary< string, int > cellsPosition, Dictionary< string, string > geneIds, string heatmapFilePath)
	Helper method that is run as a thread in BuildTextureCoroutine(List<Tuple<int, float, int>>, List<Tuple<int, float, int>>, Heatmap). More...
void	CreateHeatmapPNGScarf (Heatmap heatmap, Dictionary< string, List< Tuple< string, float >>> valueDictionary, Dictionary< string, int > genePositions, Dictionary< string, int > cellsPosition, string heatmapFilePath)
void	SavePNGtoDisk (Heatmap heatmap, string heatmapFilePath)
	If the heatmap is to be saved for logging purposes (when the user presses save heatmap) the background color should be white and text colour black for easier reading on a computer screen. So only the genelist and widths are redrawn. More...
void	AddHeatmapToList (Heatmap heatmap)

Public Attributes
ReferenceManager	referenceManager
GameObject	heatmapPrefab
GameObject	heatmapTexturePrefab
Texture2D	heatmapTexture
int	selectionNr
int	heatmapsCreated = 0
SolidBrush[]	expressionColors
SelectionManager	selectionManager
Vector3[]	startPositions

Properties
bool	GeneratingHeatmaps [get]

Detailed Description

A generator for heatmaps.

Member Function Documentation

BuildTexture() [1/3]

void CellexalVR.AnalysisLogic.HeatmapGenerator.BuildTexture	(	Cell[]	newCells,
		string[]	newGenes,
		List< Tuple< int, float, int >>	newGroupWidths,
		Heatmap	heatmap
	)

Builds this heatmaps texture using the supplied cells and genes.

Parameters

newCells	The cells that the heatmap should contain.
newGenes	The genes that the heatmap should contain.
newGroupWidths	The grouping information.

BuildTexture() [2/3]

void CellexalVR.AnalysisLogic.HeatmapGenerator.BuildTexture	(	Heatmap	heatmap,
		bool	newHeatmap = true
	)

Builds a heatmap texture based on already known groupwidths and attribute widths.

Parameters

heatmap

The heatmap to attach the texture to.

BuildTexture() [3/3]

void CellexalVR.AnalysisLogic.HeatmapGenerator.BuildTexture	(	Selection	selection,
		string	filepath,
		Heatmap	heatmap,
		bool	newHeatmap = true
	)

Builds the heatmap texture.

Parameters

selection	The selection that the heatmap was created from.
filepath	A path to the file containing the gene names

BuildTextureCoroutine()

IEnumerator CellexalVR.AnalysisLogic.HeatmapGenerator.BuildTextureCoroutine	(	Heatmap	heatmap,
		bool	newHeatmap = true
	)

Coroutine that starts a thread and generates the heatmap.

Parameters

heatmap

CreateHeatmap()

void CellexalVR.AnalysisLogic.HeatmapGenerator.CreateHeatmap

(

string

heatmapName = ""

)

Creates a new heatmap using the last confirmed selection.

Parameters

heatmapName

If created via multiplayer. Name it the same as on other client.

CreateHeatmapPNG()

void CellexalVR.AnalysisLogic.HeatmapGenerator.CreateHeatmapPNG	(	Heatmap	heatmap,
		ArrayList	result,
		Dictionary< string, int >	genePositions,
		Dictionary< string, int >	cellsPosition,
		Dictionary< string, string >	geneIds,
		string	heatmapFilePath
	)

Helper method that is run as a thread in BuildTextureCoroutine(List<Tuple<int, float, int>>, List<Tuple<int, float, int>>, Heatmap).

DeleteHeatmap()

void CellexalVR.AnalysisLogic.HeatmapGenerator.DeleteHeatmap

(

string

heatmapName

)

Removes one heatmap.

Parameters

heatmapName

The heatmap's name.

FindHeatmap()

Heatmap CellexalVR.AnalysisLogic.HeatmapGenerator.FindHeatmap

(

string

heatmapName

)

Finds a heatmap.

Parameters

heatmapName

The heatmap's name.

Returns

The heatmap, or null if no heatmap by that name exists.

HighLightGene()

void CellexalVR.AnalysisLogic.HeatmapGenerator.HighLightGene

(

string

geneName

)

Highlights gene in genelist in all the heatmaps if it is there.

Parameters

geneName

Name of the gene to be highlighted.

InitColors()

void CellexalVR.AnalysisLogic.HeatmapGenerator.InitColors

(

)

Initializes expressionColors with the colors in the config file.

SavePNGtoDisk()

void CellexalVR.AnalysisLogic.HeatmapGenerator.SavePNGtoDisk	(	Heatmap	heatmap,
		string	heatmapFilePath
	)

If the heatmap is to be saved for logging purposes (when the user presses save heatmap) the background color should be white and text colour black for easier reading on a computer screen. So only the genelist and widths are redrawn.

Parameters

heatmap	The heatmap to save.
heatmapFilePath	The filepath where to save the heatmap.

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

• cellexalvr_cloudxr/Assets/Scripts/AnalysisLogic/HeatmapGenerator.cs