| AddAdjList | Add adjacency matrix list for a PRECASTObj object | 
| AddParSetting | Add model settings for a PRECASTObj object | 
| AddTSNE | Add tSNE embeddings for a Seurat object | 
| AddUMAP | Add UMAP embeddings for a Seurat object | 
| Add_embed | Add embeddings for a Seurat object | 
| boxPlot | Boxplot for a matrix | 
| chooseColors | Choose color schema from a palette | 
| coordinate_rotate | Coordinates rotation for visualization | 
| CreatePRECASTObject | Create the PRECAST object with preprocessing step. | 
| dimPlot | Low-dimensional embeddings' plot | 
| doHeatmap | Heatmap for spots-by-feature matrix | 
| drawFigs | Draw a figure using a group of ggplot objects | 
| featurePlot | Spatial expression heatmap | 
| firstup | Set the first letter of a string vector to captial | 
| getAdj_fixedNumber | Calculate adjacency matrix by user-specified number of neighbors | 
| getAdj_reg | Calculate adjacency matrix for regular spatial coordinates. | 
| Human_HK_genes | Human housekeeping genes database | 
| ICM.EM | ICM-EM algorithm implementation | 
| ICM.EM_structure | ICM-EM algorithm implementation with organized paramters | 
| IntegrateSpaData | Integrate multiple SRT data | 
| model_set | PRECAST model setting | 
| Mouse_HK_genes | Mouse housekeeping genes database | 
| plot_RGB | Spatial RGB heatmap | 
| plot_scatter | Scatter plot for two-dimensional embeddings | 
| PRECAST | Fit a PRECAST model | 
| PRECASTObj | A simple PRECASTObj for example | 
| PRECASTObj-class | Each PRECASTObj object has a number of slots which store information. | 
| selectIntFeatures | Select common genes for multiple data batches | 
| SelectModel | Select best PRECAST model from candidated models | 
| SelectModel.PRECASTObj | Select best PRECAST model from candidated models | 
| SelectModel.SeqK_PRECAST_Object | Select best PRECAST model from candidated models | 
| SpaPlot | Spatial heatmap | 
| volinPlot | Volin/boxplot plot |