CellexalVR.AnalysisLogic Namespace Reference

Classes
class	AttributeReader
	Class that handles the reading of attribute/meta files input. More...
class	BooleanExpression
	Static class that can parse a text file with some boolean expression containing genes, facs and/or attributes.
class	BoxPlot
class	BoxPlotGrid
class	BoxPlotManager
class	Cell
	Represents one cell. A cell may be present in multiple graphs. More...
class	CellManager
	This class represent a manager that holds all the cells. More...
class	ConvexHullGenerator
class	Dataset
	Represents a loaded dataset, as well as everything that has been created from the original graphs. More...
class	GraphLoader
class	HeatmapGenerator
	A generator for heatmaps. More...
class	InputReader
	A class for reading data files and creating objects in the virtual environment. More...
class	LineBundler
	Class that handles the lines drawn between cells in different graphs and the bundling of them. More...
class	Matrix3x3
	Helper struct that defines a 3 by 3 matrix More...
class	MDSReader
	Class that handles the reading of MDS input files. Normally graph coordinates. More...
class	MoveParticleHandler
struct	MovePointComponent
class	NetworkGenerator
	This class starts the thread that generates the network files and then tells the inputreader to process them. More...
class	NetworkReader
	Class that handles the reading of correlation network input files. More...
class	NewGraphFromMarkers
	Select 3 markers and create new graph with these as axes. More...
struct	OctantData
	The data struct of a data point inside an octant. More...
class	OctantSystem
	This class handles part of the point selection logics. It divides a graph into octants and stores data in these octants so it knows which data to look for when a users selection tool is in a certain part of the graph. More...
struct	Point
	A point is the point cloud equivalent of CellexalVR.AnalysisObjects.Graph.GraphPoint. The indexes refer to the index in the position and color texture maps. More...
class	PointCloud
	A point cloud is graph that has the same functionality as Graph but is built using a visual effects graph. This because it can handle more points and animations used in slicing, spreading and streaming to reference organ. Positions and colors for the points are stored in textures. More...
struct	PointCloudComponent
class	PointCloudGenerator
	This class handles the generation of the points clouds so it is the equivalent of the CellexalVR.AnalysisObjects.GraphGenerator but for point clouds. Instantiates a point cloud prefab or spatial point cloud depending on the dataset. More...
class	PointSelectionSystem
	This class is a component system to handle the point selection in point clouds. Since the point clouds are not built using octree as the normal graphs we can not use the same selection system. But this system also in the end uses ray casts to decide if the points are inside of the selection tool. Which points are to be checked OctantSystem More...
struct	RaycastCheckComponent
	Component to add to the points that are to be raycasted and checked if they are inside the selection tool. If they are a SelectedPointComponent is added. More...
class	RaycastSystem
	This class is also part of the selection of points in a point cloud logic see also PointSelectionSystem and OctantSystem. Relevant points, meaning points that are in the same or an octant close to the users selection tool are raycasted and checked if they are outside or inside of the selection tool mesh. If they are inside they are selected, i.e. a SelectedPointComponent is added. All the logic happends inside the OnUpdate function. More...
class	ReportManager
class	RScriptRunner
	This class runs R code from a file using the console or runs a command via an R server session. More...
class	ScarfManager
	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...
struct	SelectedPointComponent
	Component struct to add to each selected point so that it can then be found and colored. More...
class	Selection
	A confirmed selection of Graph.GraphPoint. Selections are created through the SelectionManager and once done, an object of this class is created. More...
class	SelectionEnum
	Enumerator class. Required for Selection to implement IEnumerable. More...
class	SelectionManager
	Represents the selection tool that can be used to select multiple GraphPoints. More...
class	TextureHandler
	This class handles the coloring of the color texture maps of point clouds in the scene. Each point cloud has a reference to a color map where each pixel in the texture is linked to a point. This is handled via the visual effects graph. More...
struct	Vector4Int
	Helper struct that defines a vector with 4 integer components More...
class	VelocityGenerator
class	VelocityPathTool
	A tool that draws a series of lines along the average velocities of small sections of a Graph. More...