Package index • compact

All functions

ApplyPerturbation(): ApplyPerturbation

ApplyPropagation(): ApplyPropagation

BarplotShap(): Plot Bar Chart of Top SHAP Driver Genes

BeeswarmplotShap(): Plot SHAP Beeswarm Summary for Top Driver Genes

ComputeDistance(): ComputeDistance

CustomPerturbation(): CustomPerturbation

FindShapKeyDriver(): Identify Key Driver Genes Using SHAP and XGBoost

HeatmapDistance(): HeatmapDistance Generate Heatmaps for Original and Perturbed Matrices This function generates two heatmaps from two matrices (original and perturbed) and displays them side by side on the same color scale.

ModelZINB(): ModelZINB

ModulePerturbation(): ModulePerturbation

PerturbationTransitions(): PerturbationTransitions

PerturbationVectors(): Calculate Perturbation Transition Vectors for Cell Embeddings

PlotTransitionVectors(): Plot Transition Vectors on a Reduced Dimensional Embedding

ReloadShapOutput(): Reload SHAP Output from Disk

SampleZINB(): SampleZINB

TFPerturbation(): TFPerturbation

VectorFieldCoherence(): Compute Local Coherence of a Vector Field

colDeltaCor_knn(): colDeltaCor_all

.create_distance_heatmap(): This function generates a heatmap from a given matrix. It handles both matrices and data frames (converting them to matrices if needed). It also allows customization of the color palette, axis visibility, and legend display.

.edist(): edist

.eucldist(): eucldist

.get_upper_tri(): This function is used internally to extract the upper triangle of a matrix. It replaces the lower triangle of the input matrix with NA, which is useful when working with symmetrical matrices such as distance or correlation matrices where only the upper triangle is needed.