Spatial Interaction Markers
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Documentation for package ‘SpaceMarkers’ version 2.0.0
Help Pages
| .calc_IM_scores | Calculate interaction scores for a specific pattern pair |
| .calc_threshold | Compute the threshold for identifying outlier values or hotspots |
| .find_genes_of_interest | .find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes. |
| .pick_image | .pick_image |
| .row_t_test | Perform row-wise t-tests from scratch |
| calculate_gene_scores_directed | Calculate interaction scores for all pattern pairs |
| calculate_gene_set_score | calculate_gene_set_score |
| calculate_gene_set_specificity | calculate_gene_set_specificity |
| calculate_influence | Compute the spatial influence of a spatial feature |
| calculate_lr_scores | calculate_lr_scores |
| calculate_overlap_directed | calculate_overlap_directed |
| calculate_overlap_undirected | calculate_overlap_undirected |
| calculate_thresholds | Compute the thresholds for all columns in a data frame |
| curated_genes | Curated Genes for example purposes |
| find_all_hotspots | Find hotSpots for all spatial patterns |
| find_hotspots_gmm | Find hotspots for all patterns or influences based on values |
| find_pattern_hotspots | Identify hotspots of spatial pattern influence |
| get_im_scores | get_im_scores |
| get_interacting_genes | Calculate Interaction Regions and Associated Genes |
| get_pairwise_interacting_genes | get_pairwise_interacting_genes |
| get_spatial_features | Load spatial features |
| get_spatial_parameters | Read optimal parameters for spatial kernel density from user input or .json file |
| get_spatial_params_morans_i | Calculate the optimal parameters from spatial kernel density for cell-cell interactions |
| load10XCoords | Load 10x Visium Spatial Coordinates |
| load10XExpr | Load 10X Visium Expression Data |
| lrdf | Curated Ligand-receptor interaction genes A list of vectors with genes associated with ligand-receptor interactions from CellChat database |
| optParams | Optimal paramters of 5 patterns from CoGAPS. |
| plot_cell_interaction_circos | Plot Ligand-Receptor Interactions between Cell Types |
| plot_im_scores | plot_im_scores |
| plot_overlap_scores | plot_overlap_scores |
| plot_source_to_target_circos | Plot Ligand-Receptor Interactions from a Single Source to Target Cell Types |
| plot_spatial_data_over_image | plotSpatialDataOverImage |
| plot_target_from_sources_circos | Plot Ligand-Receptor Interactions from Multiple Source to a Single Target Cell Type |