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| 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 |