Package index • scDiagnostics

Visualization of Cell Type Annotations

boxplotPCA(): Plot Principal Components for Different Cell Types
calculateDiscriminantSpace() plot(<calculateDiscriminantSpaceObject>): Project Query Data onto a Unified Discriminant Space of Reference Data
calculateSIRSpace() plot(<calculateSIRSpaceObject>): Calculate Sliced Inverse Regression (SIR) Space for Different Cell Types
plotCellTypeMDS(): Plot Reference and Query Cell Types using MDS
plotCellTypePCA(): Plot Principal Components for Different Cell Types

calculateGraphIntegration() plot(<calculateGraphIntegrationObject>): Calculate Graph Community Integration Diagnostics
calculateWassersteinDistance() plot(<calculateWassersteinDistanceObject>): Compute Wasserstein Distance Distributions Between Query and Reference Datasets
comparePCA() plot(<comparePCAObject>): Compare Principal Components Analysis (PCA) Results
comparePCASubspace() plot(<comparePCASubspaceObject>): Compare Subspaces Spanned by Top Principal Components
plotPairwiseDistancesDensity(): Ridgeline Plot of Pairwise Distance Analysis

calculateAveragePairwiseCorrelation() plot(<calculateAveragePairwiseCorrelationObject>): Compute Average Pairwise Correlation between Cell Types
calculateCramerPValue(): Calculate Cramer Test P-Values for Two-Sample Comparison of Multivariate ECDFs
calculateHotellingPValue(): Perform Hotelling's T-squared Test on PCA Scores for Single-cell RNA-seq Data
calculateMMDPValue(): Calculate Maximum Mean Discrepancy P-Values for Two-Sample Comparison
plot(<regressPCObject>) regressPC(): Plot Regression Results on Principal Components

detectAnomaly() plot(<detectAnomalyObject>): PCA Anomaly Scores via Isolation Forests with Visualization
calculateReconstructionError() plot(<calculateReconstructionErrorObject>): Calculate PCA Reconstruction Errors for Out-of-Distribution Anomaly Detection
calculateCellSimilarityPCA() plot(<calculateCellSimilarityPCAObject>): Calculate Cell Similarity Using PCA Loadings

calculateCellDistances() plot(<calculateCellDistancesObject>): Compute Cell Distances Between Reference and Query Data
calculateCellDistancesSimilarity(): Function to Calculate Bhattacharyya Coefficients and Hellinger Distances

calculateHVGOverlap(): Calculate the Overlap Coefficient for Highly Variable Genes
calculateGeneShifts() plot(<calculateGeneShiftsObject>): Calculate Top Loading Gene Expression Shifts
calculateVarImpOverlap(): Compare Gene Importance Across Datasets Using Random Forest
compareMarkers() plot(<compareMarkersObject>): Compare Marker Gene Expression between Query and Reference Data

plotGeneExpressionDimred(): Visualize gene expression on a dimensional reduction plot
plotMarkerExpression(): Plot gene expression distribution from overall and cell type-specific perspective

histQCvsAnnotation(): Histograms: QC Stats and Annotation Scores Visualization
plotQCvsAnnotation(): Scatter plot: QC stats vs Cell Type Annotation Scores
plotGeneSetScores(): Visualization of gene sets or pathway scores on dimensional reduction plot