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 |