From geospatial to spatial omics


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Documentation for package ‘Voyager’ version 1.8.1

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.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