Fast Embedding Guided by Self-Organizing Map


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Documentation for package ‘EmbedSOM’ version 1.9.1

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