Man pages for edward130603/BayesSpace
Clustering and Resolution Enhancement of Spatial Transcriptomes
| BayesSpace | BayesSpace: A package for processing spatial transcriptomes |
| cluster | Wrapper around C++ 'iterate_*()' functions |
| clusterPlot | Plot spatial cluster assignments. |
| deconvolve | Wrapper around C++ 'iterate_deconv()' function |
| dot-adjust_hex_centers | Adjust hex spot positions so hexagons are adjacent to each... |
| dot-bsData | Access BayesSpace metadata |
| dot-clean_chain | Tidy C++ outputs before writing to disk. |
| dot-compute_interspot_distances | Estimate the distance between two neighboring spots |
| dot-extract_indices | Extract row and column indices of the count matrix from h5... |
| dot-find_neighbors | Find neighboring spots based on array coordinates |
| dot-flatten_matrix_list | Convert a list of matrices to a single matrix, where each row... |
| dot-flip_axis | Whether to flip x and y axis to align the plot with the... |
| dot-infer_param_dims | Infer original dimensions of parameter (per iteration) from... |
| dot-init_cluster | Initialize cluster assignments |
| dot-list2vec | Convert a list into vectors for easier output. |
| dot-make_hex_spots | Make vertices for each hex spot |
| dot-make_index_names | Make colnames for parameter indices. |
| dot-make_spot_vertices | Compute vertex coordinates for each spot in frame of plot |
| dot-make_square_spots | Make vertices for each square spot |
| dot-make_subspot_coldata | Add subspot labels and offset row/col locations before making... |
| dot-make_subspots | Define offsets and Manhattan distances for each subspot... |
| dot-make_triangle_subspots | Make vertices for each triangle subspot of a hex |
| dot-make_vertices | Make vertices outlining spots/subspots for geom_polygon() |
| dot-prepare_inputs | Prepare cluster/deconvolve inputs from SingleCellExperiment... |
| dot-read_chain | Load saved chain from disk. |
| dot-read_spot_pos | Load spot positions. |
| dot-select_spot_positions | Helper to extract x, y, fill ID from colData |
| dot-select_subspot_positions | Helper to pull out subspot position columns Probably... |
| enhanceFeatures | Predict feature vectors from enhanced PCs. |
| exampleSCE | Create minimal 'SingleCellExperiment' for documentation... |
| featurePlot | Plot spatial gene expression. |
| find_neighbors | Compute pairwise distances between all spots and return list... |
| getRDS | Download a processed sample from our S3 bucket |
| mcmcChain | Read MCMC chain associated with a BayesSpace clustering or... |
| Mode | Find the mode |
| parallelize | Parallelization |
| qTune | Tuning the choice of q (number of clusters) before running... |
| readVisium | Load a Visium spatial dataset as a SingleCellExperiment. |
| spatialCluster | Spatial clustering |
| spatialEnhance | Enhance spot resolution |
| spatialPlot | Spatial plotting functions |
| spatialPreprocess | Preprocess a spatial dataset for BayesSpace |
