Man pages for EmbedSOM
Fast Embedding Guided by Self-Organizing Map
| 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... |
| ExpressionGradient | The ggplot2 scale gradient from ExpressionPalette. |
| ExpressionPalette | Marker expression palette generator based off ColorBrewer's... |
| 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... |
| 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 |
