Man pages for shangll123/SpatialPCA
Spatially Aware Dimension Reduction for Spatial Transcriptomics
| bandwidth_select | Select bandwidth in Gaussian kernel. |
| CreateSpatialPCAObject | Create the SpatialPCA object with filtering and normalization... |
| fx_CHAOS | Calculate CHAOS score to measure clustering performance. |
| fx_PAS | Calculate PAS score to measure clustering performance. |
| get_NMF | Obtain NMF low dimensional components for dimension reduction... |
| get_PCA | Obtain PCA low dimensional components for dimension reduction... |
| kernel_build | Build kernel matrix. |
| kernel_build_sparse | Build sparse kernel matrix. |
| louvain_clustering | Obtain clustering cluster labels through louvain method. |
| plot_cluster | Visualize cluster labels on locations. |
| plot_each_cluster | Obtain each cluster label visualized on locations. |
| plot_factor_value | Visualize PCs on their locations. |
| plot_RGB_tSNE | Visualize RGB plot from tSNE. |
| plot_RGB_UMAP | Visualize RGB plot from UMAP. |
| plot_trajectory | Visualize pseudotimes on locations. |
| refine_cluster_10x | Refine clustering results for 10x ST or Visium data. |
| Spatial-package | The 'SpatialPCA' package. |
| SpatialPCA_buildKernel | Calculating kernel matrix from spatial locations. |
| SpatialPCA-class | Each SpatialPCA object has a number of slots which store... |
| SpatialPCA_EstimateLoading | Calculate loading matrix. |
| SpatialPCA_expr_pred | High-resolution gene expression prediction. |
| SpatialPCA_highresolution | High-resolution spatial map construction. |
| SpatialPCA_Multiple_Sample | Multiple sample SpatialPCA. In this extension, we construct... |
| SpatialPCA_SpatialPCs | Calculating Spatial PCs (latent factor matrix Z). |
| walktrap_clustering | Obtain clustering cluster labels through walktrap method. |
