Function reference • ProjectSVR

Class Class defined in ProjectSVR
`CellProject-class`	The CellProject class
`GridDensity-class` `GridDensity`	The GridDensity class
Object interaction Functions for interacting with objects in ProjectSVR
`SplitCellProject()`	Split CellProject Object
`merge(<CellProject>)`	Merge CellProject Objects
`newCellProject()`	Creates a new CellProject object.
`subset2()`	Subset CellProject Object
Meta cell Functions for making meta cells
`EstimateKnnDensity()`	Estimate KNN density on 2d embedding.
`MergeCells()`	Merge cells around mesh points in each bin into pseudo-bulk gene expression matrix.
`plot(<GridDensity>)`	Grid density plot
`subset(<GridDensity>)`	subset a GridDensity object.
Feature selection Functions for extract signature gene sets
`FindOptimalK()`	Find optimal components or topics for cNMF
`RunCNMF()`	Run consensus NMF
`mcFindAllMarkers()`	multi-core FindAllMarkers()
Gene module score Functions for computing gene module score
`ComputeModuleScore()`	Calculate gene module scores
Reference model construction Functions for training reference model
`FitEnsemblMultiClassif()`	Training an ensemble classifier for cell type prediction.
`FitEnsembleSVM()`	Training an ensemble SVM model for embedding coordinates regression.
Reference mapping Functions for reference mapping
`AddProjQual()`	Add projection quality scores for the query cells.
`CreateReference()`	Create reference models
`MapQuery()`	A wrapper for mapping query data onto reference.
`ProjectNewdata()`	Predicting the embedding coordinates via the trained SVM model.
`RefineProjection()`	Refine low confidence mapping coords.
Label transfer Functions for label transfer
`KnnLabelTransfer()`	Label transfer via KNN
`LabelTransfer()`	A wrapper for transferring reference cell labels to the query via KNN method.
`MajorityVote()`	Majority voting to harmonise cell labels on given over clusters
`PredictNewdata()`	Predict cell types
Differential cell population Functions for testing differential cell population
`AbundanceTest()`	Differential Cellular Abundance Test
`PercentageStat()`	Calculate cell population percentage
Visualization Functions for nice plots
`AlluviaPlot()`	Plot Alluvial Plot
`BoxPlot()`	BoxPlot
`DimTheme()`	theme for DimPlot
`GroupPreferencePlot()`	Create Group Preference Plot
`MapQCPlot()`	Visualizing the mapping quality of projected query cells.
`PlotProjection()`	Visualizing the projected query cells on reference via a density plot.
`VolcanoPlot()`	Plot the Volcano Plot
Data Descriptions of data included with ProjectSVR
`pals`	Cell type color palette
`ribo.genes`	A data set containing all human ribosomal genes
Internal Internal functions
`NNHelper()`	Internal helper function to dispatch to various neighbor finding methods
`sknn()`	Run sklearn.neighbors.NearestNeighbors

Reference

Class

Object interaction

Meta cell

Feature selection

Gene module score

Reference model construction

Reference mapping

Label transfer

Differential cell population

Visualization

Data

Internal