Package index • Voyager

Spatial statistics

calculateBivariate(<ANY>) calculateBivariate(<SpatialFeatureExperiment>) runBivariate(): Bivariate spatial statistics

calculateMultivariate(<ANY>,<SFEMethod>) calculateMultivariate(<ANY>,<character>) calculateMultivariate(<SpatialFeatureExperiment>,<ANY>) runMultivariate(): Multivariate spatial data analysis

calculateUnivariate(<ANY>,<SFEMethod>) calculateUnivariate(<ANY>,<character>) calculateUnivariate(<SpatialFeatureExperiment>,<ANY>) calculateMoransI(<ANY>) calculateMoransI(<SpatialFeatureExperiment>) colDataUnivariate() colDataMoransI() colGeometryUnivariate() colGeometryMoransI() annotGeometryUnivariate() annotGeometryMoransI() runUnivariate() runMoransI() reducedDimUnivariate() reducedDimMoransI(): Univariate spatial stiatistics

listSFEMethods(): List all spatial methods in Voyager package

moranBounds(): Compute the bounds of Moran's I given spatial neighborhood graph

multispati_rsp(): A faster implementation of MULTISPATI PCA

.variogram() .variogram_bv() .cross_variogram() .cross_variogram_map() .variogram_map(): Compute variograms

Downstream analyses of univariate spatial results

clusterCorrelograms(): Find clusters of correlogram patterns

clusterMoranPlot(): Find clusters on the Moran plot

clusterVariograms(): Cluster variograms of multiple features

Spatial plotting

ditto_colors: Colorblind friendly palette from dittoSeq

getDivergeRange(): Get beginning and end of palette to center a divergent palette

plotCellBin2D(): Plot cell density as 2D histogram

plotColGraph() plotAnnotGraph(): Plot spatial graphs

plotGeometry(): Plot geometries without coloring

plotImage(): Show image without plotting geometries

plotSpatialFeature(): Plot gene expression in space

plotTxBin2D(): Plot transcript spot density as 2D histogram

spatialReducedDim(): Plot dimension reduction components in space

Plot spatial analysis results

moranPlot(): Use ggplot to plot the moran.plot results

plotCorrelogram(): Plot correlogram

plotCrossVariogram(): Plot cross variogram

plotCrossVariogramMap(): Plot cross variogram map

plotLocalResult(): Plot local results

plotMoranMC(): Plot Moran/Geary Monte Carlo results

plotVariogram(): Plot variogram

plotVariogramMap(): Plot variogram maps

Non-spatial plotting

ElbowPlot(): Plot the elbow plot or scree plot for PCA

plotColDataFreqpoly() plotRowDataFreqpoly(): Plot frequency polygons for colData and rowData columns

plotColDataHistogram() plotRowDataHistogram(): Plot histograms for colData and rowData columns

plotDimLoadings(): Plot top PC loadings of genes

Spatial analysis results

Extensibility

SFEMethod() info(<SFEMethod>) is_local(<SFEMethod>) fun(<SFEMethod>) reorganize_fun(<SFEMethod>) args_not_check(<SFEMethod>) is_joint(<SFEMethod>) use_graph(<SFEMethod>) use_matrix(<SFEMethod>): SFEMethod class

Utilities