CellexalVR.AnalysisLogic.InputReader Class Reference

A class for reading data files and creating objects in the virtual environment. More...

Inheritance diagram for CellexalVR.AnalysisLogic.InputReader:

Public Member Functions
void	ReadFolderConsole (string path)
void	ReadScarfFolderConsole (string path)
void	ReadPreviousSessionConsole (string path, string fromPreviousSession="")
void	ReadFolder (string path, Dictionary< string, string > h5config=null, string fromPreviousSession="")
	Reads one folder of data and creates the graphs described by the data. More...
void	ReadGraphFromMarkerFile (string path, string file)
	Reads a facs marker file. More...
void	ReadFilterFiles (string path)
	Reads all saved filter files. More...
IEnumerator	StartServer (string serverType, string fromPreviousSession="")
	Start the R session that will run in the background. More...
void	QuitServer ()
	To clean up server files after termination. Can be called if the user wants to start a new session (e.g. when loading a new dataset) or when exiting the program. More...
void	ReadFacsFiles (string path)
	Reads the index.facs file. More...
void	ReadNumericalData (string path)
	Read numerical attribute data e.g. age in geomx data (not facs or gene expression those are read seperately) More...
void	ReadNetworkFiles (int layoutSeed, string path, Selection selection)
	Reads the files containg networks. More...
void	LoadPreviousGroupings ()
	Read all the user.group files which cointains the grouping information from previous sessions. More...
void	ReadAnnotationFile (string path)
	Read input from annotation file. File should contain cell ids in one column and annotation in one. More...
Selection	ReadSelectionFile (string path, bool select=true)
	Make selection from reading either previously made selection in session or an externally made selection. File contains cell ids and group colour and name of graph it was selected from. More...
void	ReadAndSelectPreviousSelection (int index)

Static Public Member Functions
static bool	CompareColor (UnityEngine.Color a, UnityEngine.Color b, float tolerance=0.1f)
	Helper function used to decide if two colors are (by some margin) equal. E.g. Used when reading in selections and deciding if a new color needs to be added or if it already exists in the config. Alpha channel is ignored. More...

Public Attributes
ReferenceManager	referenceManager
GameObject	spatialGraphPrefab
int	facsGraphCounter
bool	attributeFileRead
AttributeReader	attributeReader
MDSReader	mdsReader
PointCloudGenerator	pointCloudGenerator
Dictionary< string, H5Reader >	h5readers = new Dictionary<string, H5Reader>()
bool	debug

Detailed Description

A class for reading data files and creating objects in the virtual environment.

Member Function Documentation

CompareColor()

static bool CellexalVR.AnalysisLogic.InputReader.CompareColor ( UnityEngine.Color  a, UnityEngine.Color  b, float  tolerance = 0.1f  )

static

Helper function used to decide if two colors are (by some margin) equal. E.g. Used when reading in selections and deciding if a new color needs to be added or if it already exists in the config. Alpha channel is ignored.

Parameters

a	First color.
b	Second color.
tolerance	Function returns true if the distance between them are equal or lower than this value.

LoadPreviousGroupings()

void CellexalVR.AnalysisLogic.InputReader.LoadPreviousGroupings

(

)

Read all the user.group files which cointains the grouping information from previous sessions.

QuitServer()

void CellexalVR.AnalysisLogic.InputReader.QuitServer

(

)

To clean up server files after termination. Can be called if the user wants to start a new session (e.g. when loading a new dataset) or when exiting the program.

ReadAnnotationFile()

void CellexalVR.AnalysisLogic.InputReader.ReadAnnotationFile

(

string

path

)

Read input from annotation file. File should contain cell ids in one column and annotation in one.

Parameters

path	Path to annotation file.

ReadFacsFiles()

void CellexalVR.AnalysisLogic.InputReader.ReadFacsFiles

(

string

path

)

Reads the index.facs file.

ReadFilterFiles()

void CellexalVR.AnalysisLogic.InputReader.ReadFilterFiles

(

string

path

)

Reads all saved filter files.

Parameters

path	The directory to look for filter files in.

ReadFolder()

void CellexalVR.AnalysisLogic.InputReader.ReadFolder	(	string	path,
		Dictionary< string, string >	h5config = null,
		string	fromPreviousSession = ""
	)

Reads one folder of data and creates the graphs described by the data.

Parameters

path	The path to the folder.

ReadGraphFromMarkerFile()

void CellexalVR.AnalysisLogic.InputReader.ReadGraphFromMarkerFile	(	string	path,
		string	file
	)

Reads a facs marker file.

Parameters

path	The path to the directory
file	The path to the file.

ReadNetworkFiles()

void CellexalVR.AnalysisLogic.InputReader.ReadNetworkFiles	(	int	layoutSeed,
		string	path,
		Selection	selection
	)

Reads the files containg networks.

ReadNumericalData()

void CellexalVR.AnalysisLogic.InputReader.ReadNumericalData

(

string

path

)

Read numerical attribute data e.g. age in geomx data (not facs or gene expression those are read seperately)

Parameters

path

ReadSelectionFile()

Selection CellexalVR.AnalysisLogic.InputReader.ReadSelectionFile	(	string	path,
		bool	select = true
	)

Make selection from reading either previously made selection in session or an externally made selection. File contains cell ids and group colour and name of graph it was selected from.

Parameters

path
select

Returns

StartServer()

IEnumerator CellexalVR.AnalysisLogic.InputReader.StartServer	(	string	serverType,
		string	fromPreviousSession = ""
	)

Start the R session that will run in the background.

Parameters

serverType	If you are running several sessions give a serverType name that works as a prefix so the R session knows which file to look for.
fromPreviousSession	If you are reloading a previous session then the r object to load is found in that folder instead.

Returns

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

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