Man pages for IrisSpatialFeatures
A package to extract spatial features based on multiplex IF images
| as.data.frame | Read inForm output and store it in an IrisSpatialFeatures... |
| collapse_markers | This function collapses two markers into one, and reruns the... |
| Coordinate-class | Class to represent a single imaging coordinate |
| extract_features | Extract all spatial features |
| extract_interactions | Extract interactions between all cell-types |
| extract_mask | Read inForm output from a single coordinate |
| extract_nearest_neighbor | Extract the distance to each nearest neighbor for each... |
| extract_proximity | Run a proximity analysis on all samples. There are two modes... |
| extract_ROI | Method that reduces the current dataset to a specific region... |
| feature_selection | Function to extract all numeric features |
| get_all_interactions | Get all interactions between all cell-types |
| get_all_nearest_neighbors | Get the nearest neighbor for each cell-type |
| get_all_proximities | Get all proximity data for all cell-types in a sample |
| get_count_ratios | Get ratio of counts between two markers |
| get_counts_per_mm2 | Get all the counts on a per mm2 basis |
| get_counts_per_mm2_noncollapsed | Get all the counts on a per mm2 basis non-collapsed |
| get_interactions | Get interactions for a specific marker |
| get_nearest_neighbors | Get the nearest neighbor for a specified cell-type |
| get_proximities | Get proximity data for a given cell-type |
| ImageSet-class | Class to represent an imaging dataset. |
| interaction_maps | Plot interaction maps for all samples |
| IrisSpatialFeatures_data | Example IrisSpatialFeatures dataset |
| IrisSpatialFeatures-package | IrisSpatialFeatures: A package to extract spatial features... |
| neighbor_ray_plot | Plot nearest neighbor ray plots for each samples |
| overview_plot | Plot all coordinates in a given dataset |
| plot | Plot all frames of an IrisSpatialFeatures ImageSet object. |
| plot_interactions | Interaction summary plot for all cell-types and all samples... |
| plot_nearest_neighbor | Plot average nearest neighbor barplots for two cell types.... |
| plot_proximities | Plot proximity analysis data |
| raw_data-class | Class to represent the raw data that is output by inForm |
| rayplot_single_coordinate | Plot nearest neighbor ray plots for a single coordinate |
| read_raw | Read inForm output and store it in an IrisSpatialFeatures... |
| Sample-class | An S3 class to represent a single imaging sample with... |
| threshold_dataset | This function reads the manually determined thresholds of... |
