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:

Classes
struct	NetworkKeyPair
	Helper struct for sorting network keys. More...

Public Member Functions
void	ReadFolderConsole (string path)
void	ReadFolder (string path)
	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...
IEnumerator	ReadAttributeFilesCoroutine (string path)
	Reads an attribute file. 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...
string[][]	ReadFlashingGenesFiles (string path)
	Reads a file containing lists of genes that should be flashed. More...
void	ReadNetworkFiles (int layoutSeed)
	Reads the files containg networks. More...
void	LoadPreviousGroupings ()
	Read all the user.group files which cointains the grouping information from previous sessions. More...
void	ReadAndSelectPreviousSelection (int index)
void	SortGenesMeanExpression (ref string[] genes, ref int[][] expressions)
	Sorts a list of gene expressions based on the mean expression level. More...

Public Attributes
ReferenceManager	referenceManager
NetworkCenter	networkPrefab
TextMeshPro	graphName
GameObject	lineprefab
bool	debug = false
bool	doLoad = false

Detailed Description

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

Member Function Documentation

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.

ReadAttributeFilesCoroutine()

IEnumerator CellexalVR.AnalysisLogic.InputReader.ReadAttributeFilesCoroutine

(

string

path

)

Reads an attribute file.

Parameters

path	The path to the file.

ReadFlashingGenesFiles()

string [][] CellexalVR.AnalysisLogic.InputReader.ReadFlashingGenesFiles

(

string

path

)

Reads a file containing lists of genes that should be flashed.

Parameters

path	The path to the file.

Returns

An array of categories. Each has its name at index zero, and the rest of each array is filled with the content of the category.

ReadFolder()

void CellexalVR.AnalysisLogic.InputReader.ReadFolder

(

string

path

)

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

)

Reads the files containg networks.

SortGenesMeanExpression()

void CellexalVR.AnalysisLogic.InputReader.SortGenesMeanExpression	(	ref string[]	genes,
		ref int	expressions[][]
	)

Sorts a list of gene expressions based on the mean expression level.

Parameters

genes	An array of genes to be sorted. This array will be reordered but the elements won't be modified.
expressions	An array of arrays containing the expressions.

The expressions parameter should be set up as follows: the first dimension should be the genes and the second the cells, i.e. looking for a certain expression is done via

expressions[geneIndex][cellIndex]

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

• Assets/Scripts/AnalysisLogic/InputReader.cs