Class to handle the communication between the REST-ful scarf api and CellexalVR. The api is a flask app that gets http requests and sends back data in json format. The cellexal-scarf web api can be found here: https://github.com/sonejilab/scarf_for_cellexalvr/ More...

Inheritance diagram for CellexalVR.AnalysisLogic.ScarfManager:

Public Member Functions
void	SetZarrLoc (string loc)

void	LoadPreprocessedData (string label, string layoutKey="RNA_UMAP")

IEnumerator	LoadPreprocessedDataCouroutine (string label, string layoutKey)
	Load data into CellexalVR that has been preprocessed in scarf. More...

void	InitServer ()
	Initializes the flask app that runs the api. Start in a seperate thread. More...

IEnumerator	GetDatasetsCoroutine ()
	Retrieves the scarf datasets in the data folder. More...

IEnumerator	ConvertToZarrCoroutine (string dataLabel, string rawData)
	Convert h5 raw data to zarr format. More...

IEnumerator	StageDataCoroutine (string dataLabel)
	Prepares the scarf object to work with. More...

IEnumerator	MarkHVGSCoroutine (string topN, VisualElement running, VisualElement done)
	Calls the scarf backend function to marks highly variable genes in the staged data. More...

IEnumerator	MakeNeighborhoodGraphCoroutine (string featureKey, VisualElement running, VisualElement done)
	Calls the scarf function to create a neighborhood graph. More...

IEnumerator	RunClusteringCoroutine (string resolution, VisualElement running, VisualElement done)
	Calls the scarf function to do clustering. Requires the neighborhood graph to be made. More...

IEnumerator	RunUMAPCoroutine (string nEpochs, VisualElement running, VisualElement done)
	Calls the scarf function to create a umap. Requires the neighborhood graph to be made. More...

IEnumerator	GetFeatureNames ()
	Calls the scarf function to retrieve the feature names present in the dataset. This can be gene names or other features. More...

IEnumerator	GetCellValues (string valueKey)
	Retrieves the cell values for a specific feature key. This can be a gene or some other feature present in your dataset. More...

IEnumerator	ColorByClusters (string clusterName)
	Retrieves the cell values for the clustering and then colors the graphs accordingly. More...

IEnumerator	ColorByGene (string geneName)
	Retrieves the cell values for the given gene or other feature and then colors the graphs accordingly. More...

IEnumerator	RunMarkerSearch (string groupKey, float threshold)
	Find marker genes in the dataset. More...

IEnumerator	GetMarkers (string groupKey)
	Retrieves the marker genes. Requires RunMarkerSearch to have been run or have been marked in the dataset in pre-processing. More...

void	CloseServer ()

void	LoadData (string dataset, string key)
	Load the dataset into CellexalVR which creates the graph object. More...

Public Attributes
string[]	datasets

string[]	geneNames

string[]	markers

float[]	cellValues

bool	scarfActive

bool	reqPending

string[]	consoleLines = new string[5] { "\n", "\n ", "\n ", "\n ", "\n " }

Static Public Attributes
static ScarfManager	instance

static StringBuilder	procOutput = null

static StringBuilder	procOutput2 = null

Detailed Description

Class to handle the communication between the REST-ful scarf api and CellexalVR. The api is a flask app that gets http requests and sends back data in json format. The cellexal-scarf web api can be found here: https://github.com/sonejilab/scarf_for_cellexalvr/

Member Function Documentation

◆ ColorByClusters()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.ColorByClusters ( string clusterName )

Retrieves the cell values for the clustering and then colors the graphs accordingly.

Parameters

clusterName The name of the clustering label e.g. RNA_leiden_cluster.

Returns

◆ ColorByGene()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.ColorByGene ( string geneName )

Retrieves the cell values for the given gene or other feature and then colors the graphs accordingly.

Parameters

geneName The name of the gene or feature to color by.

Returns

◆ ConvertToZarrCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.ConvertToZarrCoroutine	(	string	dataLabel,
		string	rawData
	)

Convert h5 raw data to zarr format.

Parameters

dataLabel	What you want to call the resulting data folder.
rawData	The name of the raw data file.

Returns

◆ GetCellValues()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.GetCellValues ( string valueKey )

Retrieves the cell values for a specific feature key. This can be a gene or some other feature present in your dataset.

Parameters

valueKey The name of the feature.

Returns

◆ GetDatasetsCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.GetDatasetsCoroutine ( )

Retrieves the scarf datasets in the data folder.

Returns

◆ GetFeatureNames()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.GetFeatureNames ( )

Calls the scarf function to retrieve the feature names present in the dataset. This can be gene names or other features.

Returns

◆ GetMarkers()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.GetMarkers ( string groupKey )

Retrieves the marker genes. Requires RunMarkerSearch to have been run or have been marked in the dataset in pre-processing.

Parameters

groupKey The key used to separate the cells into groups. For example RNA_leiden clusters.

Returns

◆ InitServer()

void CellexalVR.AnalysisLogic.ScarfManager.InitServer ( )

Initializes the flask app that runs the api. Start in a seperate thread.

◆ LoadData()

void CellexalVR.AnalysisLogic.ScarfManager.LoadData	(	string	dataset,
		string	key
	)

Load the dataset into CellexalVR which creates the graph object.

Parameters

dataset
key

◆ LoadPreprocessedDataCouroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.LoadPreprocessedDataCouroutine	(	string	label,
		string	layoutKey
	)

Load data into CellexalVR that has been preprocessed in scarf.

Parameters

label	Name of the dataset folder.
layoutKey	Name of the value you wish to plot. For example if you have made a umap based on RNA data it is usually called RNA_UMAP. Or whatever else you have named it when pre-processing the data.

Returns

◆ MakeNeighborhoodGraphCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.MakeNeighborhoodGraphCoroutine	(	string	featureKey,
		VisualElement	running,
		VisualElement	done
	)

Calls the scarf function to create a neighborhood graph.

Parameters

featureKey	The feature key in the scarf object to use to create the graph. E.g. hvgs (if you have marked hvgs that is.)
running	For the user interface icons animation.
done	For the user interface icons animation.

Returns

◆ MarkHVGSCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.MarkHVGSCoroutine	(	string	topN,
		VisualElement	running,
		VisualElement	done
	)

Calls the scarf backend function to marks highly variable genes in the staged data.

Parameters

topN	Number of genes.
running	For the user interface icons animation.
done	For the user interface icons animation.

Returns

◆ RunClusteringCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.RunClusteringCoroutine	(	string	resolution,
		VisualElement	running,
		VisualElement	done
	)

Calls the scarf function to do clustering. Requires the neighborhood graph to be made.

Parameters

resolution	Resolution of clustering. Corresponding to the argument with the same name in the scarf clustering function.
running	For the user interface icons animation.
done	For the user interface icons animation.

Returns

◆ RunMarkerSearch()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.RunMarkerSearch	(	string	groupKey,
		float	threshold
	)

Find marker genes in the dataset.

Parameters

groupKey	The key used to separate the cells into groups. For example RNA_leiden clusters.
threshold	Threshold to use for a gene correlation.

Returns

◆ RunUMAPCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.RunUMAPCoroutine	(	string	nEpochs,
		VisualElement	running,
		VisualElement	done
	)

Calls the scarf function to create a umap. Requires the neighborhood graph to be made.

Parameters

nEpochs	Number of epochs to run.
running	For the user interface icons animation.
done	For the user interface icons animation.

Returns

◆ StageDataCoroutine()

IEnumerator CellexalVR.AnalysisLogic.ScarfManager.StageDataCoroutine ( string dataLabel )

Prepares the scarf object to work with.

Parameters

dataLabel

Returns

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

cellexalvr_cloudxr/Assets/Scripts/AnalysisLogic/ScarfManager.cs

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Member Function Documentation

◆ ColorByClusters()

◆ ColorByGene()

◆ ConvertToZarrCoroutine()

◆ GetCellValues()

◆ GetDatasetsCoroutine()

◆ GetFeatureNames()

◆ GetMarkers()

◆ InitServer()

◆ LoadData()

◆ LoadPreprocessedDataCouroutine()

◆ MakeNeighborhoodGraphCoroutine()

◆ MarkHVGSCoroutine()

◆ RunClusteringCoroutine()

◆ RunMarkerSearch()

◆ RunUMAPCoroutine()

◆ StageDataCoroutine()