Man pages for PRECAST
Embedding and Clustering with Alignment for Spatial Datasets
| AddAdjList | Add adjacency matrix list for a PRECASTObj object |
| Add_embed | Add embeddings for a Seurat 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 |
| boxPlot | Boxplot for a matrix |
| chooseColors | Choose color schema from a palette |
| coordinate_rotate | Coordinates rotation for visualization |
| CreateiDRSCObject | 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... |
| getAdj_reg | Calculate adjacency matrix for regular spatial coordinates. |
| Human_HK_genes | Human housekeeping genes database |
| ICM.EM_structure | ICM-EM algorithm implementation with organized paramters |
| idrsc | ICM-EM algorithm implementation |
| 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 |
| PObj | A simple PRECASTObj for example |
| PRECAST | Fit a PRECAST model |
| PRECASTObj | Each PRECASTObj object has a number of slots which store... |
| selectIntFeatures | Select common genes for multiple data batches |
| selectModel | Select best PRECAST model from candidated models |
| SpaPlot | Spatial heatmap |
| volinPlot_real | Volin/boxplot plot |
