# Fast Embedding Guided by Self-Organizing Map

## Documentation for package ‘EmbedSOM’ version 2.1.1

- 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