Fast Embedding Guided by Self-Organizing Map

---

Documentation for package ‘EmbedSOM’ version 2.1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ClusterPalette	An acceptable cluster color palette
EmbedSOM	Process the cells with SOM into a nice embedding
ExprColors	Generate colors for multi-color marker expression labeling in a single plot
ExpressionGradient	The ggplot2 scale gradient from ExpressionPalette.
ExpressionPalette	Marker expression palette generator based off ColorBrewer's RdYlBu, only better for plotting of half-transparent cells
GQTSOM	Train a Growing Quadtree Self-Organizing Map
GraphCoords	Add Kamada-Kawai-generated embedding coordinates to the map
Initialize_PCA	Create a grid from first 2 PCA components
kMeansMap	Create a map from k-Means clusters
kNNCoords	Add KNN-topology-based embedding coordinates to the map
MapDataToCodes	Assign nearest node to each datapoint
MSTCoords	Add MST-style embedding coordinates to the map
NormalizeColor	Helper for computing colors for embedding plots
PlotData	Export a data frame for plotting with marker intensities and density.
PlotDefault	Default plot
PlotEmbed	Helper function for plotting the embedding
PlotGG	Wrap PlotData result in ggplot object.
PlotId	Identity on whatever
RandomMap	Create a map by randomly selecting points
SOM	Build a self-organizing map
tSNECoords	Add tSNE-based coordinates to a map
UMAPCoords	Add UMAP-based coordinates to a map
UMatrixCoords	Add U-Matrix-optimized embedding coordinates to the map
uwotCoords	Add UMAP-based coordinates to a map, using the 'uwot' package