Man pages for gusef/Iris
A package to extract spatial features based on multiplex IF images
| aggregated_nn_data_frame | Dump the nearest neighbor data that was extracted |
| as.data.frame | Get the dataframe from a normalized nearest neighbor object. |
| binned_gated_nn_data_frame | Extract and dump nearest neighbor raw data |
| collapse_markers | This function collapses two markers into one, and reruns the... |
| compare_normalized_nearest_neighbor | Compare distances between two markers to a reference marker. |
| Coordinate-class | Class to represent a single imaging coordinate |
| counts_data_frame | DataFrame from all the counts per frame |
| counts_per_mm2_data_frame | DataFrame from all the counts on a per mm2 basis... |
| counts_per_mm2_sample_data_frame | DataFrame from all the counts on a per mm2 basis per sample |
| counts_sample_data_frame | DataFrame from all the counts per frame |
| 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_counts_data_frame | DataFrame from all the interaction counts on a per mm2 basis... |
| interaction_counts_sample_data_frame | DataFrame from all the interaction counts on a per mm2 basis... |
| interaction_maps | Plot interaction maps for all samples |
| interaction_permutation_test | Calculate a permutation test result for nearest neighbors to... |
| interaction_proportion_comparison_permutation_test | Calculate a permutation test result for nearest neighbors to... |
| interaction_proportion_data_frame | DataFrame from all the interaction proportions freshly... |
| interactions_sample_data_frame | DataFrame from all the counts on a per mm2 basis per sample |
| IrisSpatialFeatures_data | Example IrisSpatialFeatures dataset |
| IrisSpatialFeatures-package | IrisSpatialFeatures: A package to extract spatial features... |
| multiple_proximity_sample_data_frame | Extract proximity for a range of distances. Pass an array of... |
| neighbor_ray_plot | Plot nearest neighbor ray plots for each samples |
| nn_comparison_dataframe | Compare nearest neighbors by a data.frame |
| nn_comparison_permutation_test | Calculate a permutation test result for nearest neighbors to... |
| nn_data_frame | Extract and dump nearest neighbor raw data |
| NNN-class | Class to represent a normalized nearest neighbor. |
| NNN_Compare-class | Class to represent a comparison of two markers to a... |
| nn.test | Calculate Nearest Neighbor for testing outputs |
| normal_nearest_neighbor | Extract the distance to each nearest neighbor for specified... |
| normal_nearest_neighbor_sample | Extract the distance to each nearest neighbor for specified... |
| normal_nearest_neighbor_sample_once | Extract the distance to each nearest neighbor for specified... |
| 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_nnn | Plot the normalized nearest neighbor (called internally) |
| plot_proximities | Plot proximity analysis data |
| proximity_sample_data_frame | Return a data frame of the per-sample proximities like those... |
| 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... |
| shuffle_labels | shuffle labels of each frame |
| threshold_dataset | This function reads the manually determined thresholds of... |
