Man pages for EmbedSOM
Fast Embedding Guided by Self-Organizing Map

ClusterPaletteAn acceptable cluster color palette
EmbedSOMProcess the cells with SOM into a nice embedding
ExprColorsGenerate colors for multi-color marker expression labeling in...
ExpressionGradientThe ggplot2 scale gradient from ExpressionPalette.
ExpressionPaletteMarker expression palette generator based off ColorBrewer's...
GQTSOMTrain a Growing Quadtree Self-Organizing Map
GraphCoordsAdd Kamada-Kawai-generated embedding coordinates to the map
Initialize_PCACreate a grid from first 2 PCA components
kMeansMapCreate a map from k-Means clusters
kNNCoordsAdd KNN-topology-based embedding coordinates to the map
MapDataToCodesAssign nearest node to each datapoint
MSTCoordsAdd MST-style embedding coordinates to the map
NormalizeColorHelper for computing colors for embedding plots
PlotDataExport a data frame for plotting with marker intensities and...
PlotDefaultDefault plot
PlotEmbedHelper function for plotting the embedding
PlotGGWrap PlotData result in ggplot object.
PlotIdIdentity on whatever
RandomMapCreate a map by randomly selecting points
SOMBuild a self-organizing map
tSNECoordsAdd tSNE-based coordinates to a map
UMAPCoordsAdd UMAP-based coordinates to a map
UMatrixCoordsAdd U-Matrix-optimized embedding coordinates to the map
uwotCoordsAdd UMAP-based coordinates to a map, using the 'uwot' package
EmbedSOM documentation built on July 5, 2022, 5:14 p.m.