# From geospatial to spatial omics

## Documentation for package ‘Voyager’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
colFeatureData | Get metadata of colData, rowData, and geometries
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
geometryFeatureData | Get metadata of colData, rowData, and geometries
getDivergeRange | Get beginning and end of palette to center a divergent palette
getParams | Get parameters used in spatial methods
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
listw2sparse | Convert listw into sparse adjacency matrix
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
multi_listw2sparse | Convert multiple listw graphs into a single sparse adjacency matrix
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
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
plotVariogram | Plot variogram
plotVariogramMap | Plot variogram maps
reducedDimFeatureData | Get metadata of colData, rowData, and geometries
reducedDimMoransI | Univariate spatial stiatistics
reducedDimUnivariate | Univariate spatial stiatistics
reorganize_fun | SFEMethod class
reorganize_fun-method | SFEMethod class
rowFeatureData | Get metadata of colData, rowData, and geometries
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