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... |

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