From geospatial to spatial omics
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Documentation for package ‘Voyager’ version 1.11.0
Help Pages
| .cross_variogram | Compute variograms |
| .cross_variogram_map | Compute variograms |
| .variogram | Compute variograms |
| .variogram_bv | Compute variograms |
| .variogram_map | Compute variograms |
| annotGeometryMoransI | Univariate spatial stiatistics |
| annotGeometryUnivariate | Univariate spatial stiatistics |
| args_not_check | SFEMethod class |
| args_not_check-method | SFEMethod class |
| calculateBivariate | Bivariate spatial statistics |
| calculateBivariate-method | Bivariate spatial statistics |
| calculateMoransI | Univariate spatial stiatistics |
| calculateMoransI-method | Univariate spatial stiatistics |
| calculateMultivariate | Multivariate spatial data analysis |
| calculateMultivariate-method | Multivariate spatial data analysis |
| calculateUnivariate | Univariate spatial stiatistics |
| calculateUnivariate-method | Univariate spatial stiatistics |
| clusterCorrelograms | Find clusters of correlogram patterns |
| clusterMoranPlot | Find clusters on the Moran plot |
| clusterVariograms | Cluster variograms of multiple features |
| colDataMoransI | Univariate spatial stiatistics |
| colDataUnivariate | Univariate spatial stiatistics |
| colGeometryMoransI | Univariate spatial stiatistics |
| colGeometryUnivariate | Univariate spatial stiatistics |
| ditto_colors | Colorblind friendly palette from dittoSeq |
| ElbowPlot | Plot the elbow plot or scree plot for PCA |
| fun | SFEMethod class |
| fun-method | SFEMethod class |
| getDivergeRange | Get beginning and end of palette to center a divergent palette |
| info | SFEMethod class |
| info-method | SFEMethod class |
| is_joint | SFEMethod class |
| is_joint-method | SFEMethod class |
| is_local | SFEMethod class |
| is_local-method | SFEMethod class |
| listSFEMethods | List all spatial methods in Voyager package |
| moranBounds | Compute the bounds of Moran's I given spatial neighborhood graph |
| moranPlot | Use ggplot to plot the moran.plot results |
| multispati_rsp | A faster implementation of MULTISPATI PCA |
| plotAnnotGraph | Plot spatial graphs |
| plotCellBin2D | Plot cell density as 2D histogram |
| plotColDataFreqpoly | Plot frequency polygons for colData and rowData columns |
| plotColDataHistogram | Plot histograms for colData and rowData columns |
| plotColGraph | Plot spatial graphs |
| plotCorrelogram | Plot correlogram |
| plotCrossVariogram | Plot cross variogram |
| plotCrossVariogramMap | Plot cross variogram map |
| plotDimLoadings | Plot top PC loadings of genes |
| plotGeometry | Plot geometries without coloring |
| plotImage | Show image without plotting geometries |
| plotLocalResult | Plot local results |
| plotMoranMC | Plot Moran/Geary Monte Carlo results |
| plotRowDataFreqpoly | Plot frequency polygons for colData and rowData columns |
| plotRowDataHistogram | Plot histograms for colData and rowData columns |
| plotSpatialFeature | Plot gene expression in space |
| plotTxBin2D | Plot transcript spot density as 2D histogram |
| plotVariogram | Plot variogram |
| plotVariogramMap | Plot variogram maps |
| reducedDimMoransI | Univariate spatial stiatistics |
| reducedDimUnivariate | Univariate spatial stiatistics |
| reorganize_fun | SFEMethod class |
| reorganize_fun-method | SFEMethod class |
| runBivariate | Bivariate spatial statistics |
| runMoransI | Univariate spatial stiatistics |
| runMultivariate | Multivariate spatial data analysis |
| runUnivariate | Univariate spatial stiatistics |
| SFEMethod | SFEMethod class |
| SFEMethod-class | SFEMethod class |
| spatialReducedDim | Plot dimension reduction components in space |
| use_graph | SFEMethod class |
| use_graph-method | SFEMethod class |
| use_matrix | SFEMethod class |
| use_matrix-method | SFEMethod class |
| variogram-internal | Compute variograms |