This class represents a heatmap. Contains methods for calling r-script, building texture and interaction methods etc. More...

Inheritance diagram for CellexalVR.AnalysisObjects.Heatmap:

Classes
class	HeatmapLayout

Public Member Functions
void	Init ()
	Initialises the interactive elements in the heatmap and sets some necessary references. More...

void	CreateHeatmapAnimation ()

void	DeleteHeatmap ()
	Starts the deletion of heatmap. Same animation as when minimizing but destroying the object once minimized. More...

void	ResetHeatmapHighlight ()
	Removes the highlight box and the highlight text. More...

void	HighLightGene (string geneName)
	Highlights a gene in the genelist if it is there. For example when colouring from keyboard it draws attention to the gene in the list. More...

void	CreateNewHeatmapFromSelection (int selectedGroupLeft, int selectedGroupRight, int selectedGeneTop, int selectedGeneBottom, float selectedBoxWidth, float selectedBoxHeight)
	Creates a new heatmap based on what was selected on this heatmap. More...

void	UpdateAttributeWidhts ()
	Helper function to update the attribute bar widths. Used when creating a new hm from selection on old or moving groups around. More...

void	AddAttributeWidth (string attributeName, float cellWidth, Cell cell)
	Helper function to add attribute width and colour. More...

void	ReorderByAttribute ()
	Reorders the heatmap so that each selection group is reordered based on the attributes. Cells will be reordered so cells with the same attribute within the same group is next to each other. More...

void	SaveImage ()
	Saves the image used to create this heatmap to another directory. The saved image will have the a name based on when the image is saved. More...

void	DumpGenesToTextFile (string[] genes, string name)
	Dumps the genes into a text file. More...

void	UpdateImage (string filepath)
	Updates this heatmap's image. More...

void	ColorCells ()
	Recolours all graphs with the colors that the cells had when this heatmap was created. Graph points that are not part of this heatmap are not recoloured and will keep their colour. More...

void	SetVars (Dictionary< Cell, int > colors)
	Sets some variables. Should be called after a heatmap is instantiated. More...

void	CumulativeRecolorFromSelection (int selectedGroupLeft, int selectedGroupRight, int selectedGeneTop, int selectedGeneBottom)
	Recolours the graphs based on the currently selected area on the heatmap. All cells in all graphs are coloured based on the median expression of the selected genes. More...

Public Attributes
ReferenceManager	referenceManager

TextMeshPro	statusText

TextMeshPro	barInfoText

SaveHeatmapButton	saveImageButton

GOanalysisButton	goAnalysisButton

GameObject	highlightQuad

GameObject	highlightGeneQuad

GameObject	confirmQuad

GameObject	movingQuadX

GameObject	movingQuadY

TextMeshPro	enlargedGeneText

TextMeshPro	highlightGeneText

TextMeshPro	highlightInfoText

bool	removable

string	directory

Selection	selection

List< Tuple< int, float, int > >	groupWidths
	Item1: group number, Item2: group width in coordinates, Item3: number of cells in the group More...

List< Tuple< int, float, int > >	attributeWidths

List< Tuple< Cell, int > >	cellAttributes

Dictionary< int, UnityEngine.Color >	groupingColors

Dictionary< int, UnityEngine.Color >	attributeColors

Cell[]	cells

bool	orderedByAttribute = false

bool	buildingTexture = false

string[]	genes

HeatmapLayout	layout

Vector3	startPosition

Detailed Description

This class represents a heatmap. Contains methods for calling r-script, building texture and interaction methods etc.

Member Function Documentation

◆ AddAttributeWidth()

void CellexalVR.AnalysisObjects.Heatmap.AddAttributeWidth	(	string	attributeName,
		float	cellWidth,
		Cell	cell
	)

Helper function to add attribute width and colour.

◆ ColorCells()

void CellexalVR.AnalysisObjects.Heatmap.ColorCells ( )

Recolours all graphs with the colors that the cells had when this heatmap was created. Graph points that are not part of this heatmap are not recoloured and will keep their colour.

◆ CreateNewHeatmapFromSelection()

void CellexalVR.AnalysisObjects.Heatmap.CreateNewHeatmapFromSelection	(	int	selectedGroupLeft,
		int	selectedGroupRight,
		int	selectedGeneTop,
		int	selectedGeneBottom,
		float	selectedBoxWidth,
		float	selectedBoxHeight
	)

Creates a new heatmap based on what was selected on this heatmap.

◆ CumulativeRecolorFromSelection()

void CellexalVR.AnalysisObjects.Heatmap.CumulativeRecolorFromSelection	(	int	selectedGroupLeft,
		int	selectedGroupRight,
		int	selectedGeneTop,
		int	selectedGeneBottom
	)

Recolours the graphs based on the currently selected area on the heatmap. All cells in all graphs are coloured based on the median expression of the selected genes.

Parameters

selectedGroupLeft	The index of the left-most selected group.
selectedGroupRight	The index of the right-most selected group.
selectedGeneTop	The index of the top-most selected gene.
selectedGeneBottom	The index of the bottom-most selected gene.

◆ DeleteHeatmap()

void CellexalVR.AnalysisObjects.Heatmap.DeleteHeatmap ( )

Starts the deletion of heatmap. Same animation as when minimizing but destroying the object once minimized.

◆ DumpGenesToTextFile()

void CellexalVR.AnalysisObjects.Heatmap.DumpGenesToTextFile	(	string[]	genes,
		string	name
	)

Dumps the genes into a text file.

◆ HighLightGene()

void CellexalVR.AnalysisObjects.Heatmap.HighLightGene ( string geneName )

Highlights a gene in the genelist if it is there. For example when colouring from keyboard it draws attention to the gene in the list.

Parameters

geneName The name of the gene.

◆ Init()

void CellexalVR.AnalysisObjects.Heatmap.Init ( )

Initialises the interactive elements in the heatmap and sets some necessary references.

◆ ReorderByAttribute()

void CellexalVR.AnalysisObjects.Heatmap.ReorderByAttribute ( )

Reorders the heatmap so that each selection group is reordered based on the attributes. Cells will be reordered so cells with the same attribute within the same group is next to each other.

◆ ResetHeatmapHighlight()

void CellexalVR.AnalysisObjects.Heatmap.ResetHeatmapHighlight ( )

Removes the highlight box and the highlight text.

◆ SaveImage()

void CellexalVR.AnalysisObjects.Heatmap.SaveImage ( )

Saves the image used to create this heatmap to another directory. The saved image will have the a name based on when the image is saved.

◆ SetVars()

void CellexalVR.AnalysisObjects.Heatmap.SetVars ( Dictionary< Cell, int > colors )

Sets some variables. Should be called after a heatmap is instantiated.

◆ UpdateAttributeWidhts()

void CellexalVR.AnalysisObjects.Heatmap.UpdateAttributeWidhts ( )

Helper function to update the attribute bar widths. Used when creating a new hm from selection on old or moving groups around.

◆ UpdateImage()

void CellexalVR.AnalysisObjects.Heatmap.UpdateImage ( string filepath )

Updates this heatmap's image.

Member Data Documentation

◆ groupWidths

List<Tuple<int, float, int> > CellexalVR.AnalysisObjects.Heatmap.groupWidths

Item1: group number, Item2: group width in coordinates, Item3: number of cells in the group

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

cellexalvr_cloudxr/Assets/Scripts/AnalysisObjects/Heatmap.cs

Classes

Public Member Functions

Public Attributes