Man pages for patrickCNMartin/Vesalius
Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data
| add_active_count_tag | add active count tag |
| add_active_embedding_tag | add active embedding tag |
| add_counts | Add counts to vesalius assay Adding custom count matrix to a... |
| add_embeddings | Add embeddings Add custom embeddings to vesalius objects |
| adjust_counts | adjust count |
| align_index | assign coordinates to matched indices |
| assign_centers | assign centroid values to active embedding |
| average_embed | average image stack between seed and query |
| back_infer | Infer normalized counts from shared embedding values |
| bubble_stack | importFrom imager nPix |
| build_mapped_assay | Build a new vesalius_assay object using mapping information |
| build_vesalius_assay | build vesalius assay object |
| calculate_scale | calculate scale of assay |
| cell_type_match | Compute score based on cell type labels |
| check_barcodes | checking overlap between barcodes in counts and coordinates |
| check_binary_nature | check binary nature |
| check_cells | check if provided cells are contained withing provided... |
| check_coordinates | check if coordinates are of the correct type and format and... |
| check_counts | check if counts are of the correct type and format |
| check_deg_method | check if DEG method is one of the available options |
| check_dim_selection_method | check dimension selection method |
| check_embeddings | check embeddings checking user provided embedding matrix |
| check_embedding_selection | check embedding selection |
| check_embed_methods | check if embedding method is present in availble options |
| check_eq_method | check if eq method are avilable |
| check_features | check features |
| check_for_zero_counts | check_for_zero_counts check which barcodes contain all 0... |
| check_group_value | check if requested territory is in territory list |
| check_image | check if image is present |
| check_image_input | check image input check if input image is in correct format |
| check_inputs | check input checks the validity of input data to... |
| check_isolation_method | check territory isolation method is available |
| check_min_spatial_index | check number of spatial indices present |
| check_norm | check if select norm method is an available option |
| check_norm_methods | check if norm method is present in availble options |
| check_segmentation_method | check if segmentation options are valid for segmentation |
| check_segment_trial | check if segment selection is a valid option |
| check_smoothing_kernel | check if smoothing method is present in availble options |
| check_smoothing_level | check if across level options are valid for smoothing |
| check_tensor_compression | check tensor compression |
| check_territory_trial | check if territory selection is a valid option |
| check_tiles | check tile integretiy |
| commit_log | commits function call to log slot |
| compute_effect_size | compute_effect_size |
| compute_nearest_neighbor_graph | compute and greate nearest neighbor graph |
| concat_cost | concat cost - pairwise sum of score complement |
| concat_embed | create new embedding from jointly measure spatial omics |
| concat_matches | merging batch matches together |
| convexify | convexify |
| coordinates | Spatial coordinates |
| counts | Count matrix for vesalius |
| create_alpha | create alpha value if territories need to be highlighted |
| create_commit_log | create function log to be commit to the log slot |
| create_palette | create color palette from predefine scheme |
| create_pseudo_centroids | create centroid vlues for louvain and leiden |
| create_trial_tag | create a trail tag name |
| detect_edges | detect_edges detect territory edges in black and white images... |
| dispatch_batch | Dispatch cells into batches |
| dispatch_cost_groups | dispatch barcodes to subset cost for match clustering |
| dispatch_deg_group | dispatch barcodes to seed and query groups |
| dispatch_sample | dispatch barcodes associted with a specific territory in a... |
| dispatch_territory | dispatch territories labels territories according to which... |
| distance_pooling | distance pooling beads of colour segment into seperate... |
| ecdf_eq | internal ecdf eq used for formatting |
| embed_latent_space | embed latent space |
| embed_lsi | embed lsi |
| embed_lsi_umap | embed lsi |
| embed_nmf | embed nmf |
| embed_pca | embed PCA |
| embed_pcal | embed PCA loading values |
| embed_umap | embed umap |
| equalize_image | equalise image histogram |
| extend_boundary | extend image boundary around territory |
| filter_grid | filter grid |
| filter_maps | filter mapped cells |
| filter_tiles | filter tiles |
| format_call | format function call to list for log update |
| format_counts_for_deseq2 | format counts for DESeq |
| format_counts_for_edger | format counts for edgeR |
| format_counts_for_logit | format counts for logistic regression |
| format_c_to_ves | convert cimg list to vesalius object embedding |
| format_ves_to_c | convert vesalius_assay to cimg images |
| future_ves_to_cimg | convert ves embedding to image |
| generate_embeddings | Generate embeddings. |
| generate_spix | Generate super pixels from ST |
| generate_tiles | generate tiles |
| get_active_count_tag | get last count matrix used |
| get_active_embedding_tag | get active embedding |
| get_assay_names | get assay names from vesalius_assay |
| get_coordinayes | get coordinates from vesalius_assay |
| get_cost_contribution | Compute mapping score contribution to mapping |
| get_counts | get counts from vesalius_assay |
| get_deg_metrics | get DEG metrics from groups |
| get_embeddings | get embeddings from vesalius_assay |
| get_func_from_commit | get function name from commit list |
| get_markers | get markers from vesalius_assay |
| get_metric_clusters | Cluster query cells based on which reference cells they tend... |
| get_neighborhood_signal | Method dispatch function for neighborhood selection |
| get_signal | get cell signal from vesalius assays |
| get_territories | get territories from vesalius_assay |
| get_tiles | get tiles from vesalius_assay |
| globalise_territories | globalise territories converts territories number from... |
| graph_neighborhood | Graph depth method based method to select niche |
| graph_path_length | get path length in a graph |
| hclust_scores | Hiearchal clustering of mapping scores for co mapping events |
| identify_markers | identify_markers computes differential observation expression... |
| image_plot | image_plot - plotting vesalius embeddings |
| initialize_matches | initialize matched data frame |
| integrate_assays | integrate 2 vesalius assays |
| integrate_counts | Integrate counts using Seurat |
| interlace_embeds | interlace image stack between seed and query |
| internal_smooth | internal smoothing function Function that does the smoothing... |
| int_sctransform | SCTransform |
| isolate_territories | isolating territories from vesalius image segments |
| jitter_coord | Spatial coordinates - alt |
| jitter_counts | Count matrix for vesalius - alt |
| joint_territories | Jointly measured spatial omic assays territories |
| kmeans_segmentation | kmeans segmentation function |
| knn_neighborhood | k nearest neighbors - niche selection |
| layer_territory | layer_territory generates layer from the outside to the... |
| leiden_scores | Using Leiden community clustering to for co-mapping events |
| leiden_segmentation | leiden segmentation |
| log_norm | log norm |
| louvain_scores | Using Louvain community clustering to for co-mapping events |
| louvain_segmentation | louvain segmentation |
| map_assays | Aling and integrate spatial assay from the same modality... |
| map_index | LAPVJ solver |
| match_cells | Internal function returning cell type label match as numiric |
| merge_coordinates | Merge coordinates from 2 vesalius assays |
| merge_territories | Merge territories using specified labels |
| message_switch | switch message output based in input |
| min_max | min max normalisation |
| neighborhood_signal | compute average expression of local neighborhood |
| niche_composition | Method dispatch function for neighborhood selection - added... |
| no_norm | no norm |
| norm_pixel | pixel normalisation dispatch function |
| optimize_matching | optimize matching scores through batching |
| overlap_distance_matrix | create a distance matrix based on mapping scores overlaps |
| pearson_approx | compute fast pearson correlation between matrices |
| point_mapping | mapping points between data sets |
| populate_graph | populate graph with network connections |
| process_counts | process counts |
| radius_neighborhood | Radius based method to select niche |
| rasterise | rasterise tiles |
| rebalence_colors | rebalence colors |
| reduce_tensor_resolution | reduce tensor resoltuon |
| regularise | Internal regularise function. performs total variance... |
| regularise_image | regularise image |
| rename_counts | renaming counts to remain consistent with vesalius... |
| score_matches | Extract score from best matches |
| search_log | search through log for parameter values or names |
| segment_image | segment image |
| select_initial_indices | select inital indices |
| signal_similarity | compute the similarity between seed and query signals |
| smooth_image | Smooth Image |
| summarise_territories | summarise territories |
| territory_morphing | territory_morphing applies morphological operators to a set... |
| territory_neighborhood | Territory selection for large scale niche |
| territory_plot | territory_plot - plotting Vesalius territories |
| tfidf_norm | tf idf normalisation |
| unpack_territory_path | retrieve the points contained in the edge of each territory |
| update_matches | Update best matched cell pairs with new mapping costs |
| update_vesalius_assay | update vesalius assay object |
| vesalius_assay-class | The vesalius_assay class |
| vesalius_deg | Internal differantial gene expression function. |
| vesalius_deg_chisq | chisq test for DEG |
| vesalius_deg_deseq2 | DESeq negatove binomail for DEG |
| vesalius_deg_edger | edgeR functions for DEG |
| vesalius_deg_fisher | Fisher's excat test for DEG |
| vesalius_deg_logit | Logistic Regression for DEG |
| vesalius_deg_ttest | t.test for DEG |
| vesalius_deg_wilcox | wilcox rank sum test for DEG |
| vesalius_package | vesalius |
| view_gene_expression | view_gene_expression |
