# Fast Embedding Guided by Self-Organizing Map

## Documentation for package ‘EmbedSOM’ version 1.9.1

- 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
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
Initialize_PCA | Create a grid from first 2 PCA components
MapDataToCodes | Assign nearest node to each datapoint
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
SOM | Build a self-organizing map