Coordinate-class        Class to represent a single imaging coordinate
ImageSet-class          Class to represent an imaging dataset.
IrisSpatialFeatures     IrisSpatialFeatures: A package to extract
                        spatial features based on multiplex IF images
IrisSpatialFeatures_data
                        Example IrisSpatialFeatures dataset
Sample-class            An S3 class to represent a single imaging
                        sample with multiple coordinates.
as.data.frame,ImageSet-method
                        Read inForm output and store it in an
                        IrisSpatialFeatures ImageSet object.
collapse_markers        This function collapses two markers into one,
                        and reruns the counting of cells. Mostly a
                        convenience function for the Shiny interface so
                        we start with a completely split set
                        successively adding more markers
extract_ROI             Method that reduces the current dataset to a
                        specific region of interest, discarding all
                        cell coordinates outside of that region
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 cell-type
extract_proximity       Run a proximity analysis on all samples. There
                        are two modes this function can be run. In the
                        first mode it uses the major and minor axes for
                        each cell as provided by inform. It then
                        averages half of those two axes and adds an
                        uncertainty margin, which are used to provide
                        an estimate on whether two cells are touching.
                        This mode can be used to approximate the
                        interaction analysis. The second mode uses a
                        user specified distance to count the cells
                        within the proximity of a given cell-type. With
                        increasing distances usually cells fall into
                        the proximity of multiple cells of a given type
                        so the function allows the restriction of only
                        counting the cell only once.
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
interaction_maps        Plot interaction maps for all samples
neighbor_ray_plot       Plot nearest neighbor ray plots for each
                        samples
overview_plot           Plot all coordinates in a given dataset
plot,ImageSet-method    Plot all frames of an IrisSpatialFeatures
                        ImageSet object.
plot_interactions       Interaction summary plot for all cell-types and
                        all samples in a dataset
plot_nearest_neighbor   Plot average nearest neighbor barplots for two
                        cell types. This measurement is not symmetric,
                        so if 'from' and 'to' are switched it will
                        result in different results. For the 'to'
                        parameter this function allows a cell-type
                        without '+' or '-' in the end. Indicating that
                        the distances from the first cell-type should
                        be calculated against both '+/-' and a paired
                        t-test should be calculated. For example we
                        want to calculate the average distance between
                        SOX10 PDL1+ melanoma cells against both CD8
                        PD1+ and CD8 PD1- cells, the 'CD8 PD1' would be
                        speficified as 'to' parameter, 2 distances
                        would be calculated for each sample and a
                        two-sided paired t-test calculated to test for
                        significant differences.
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 ImageSet object.
threshold_dataset       This function reads the manually determined
                        thresholds of certain markers (e.g. PD1, PD-L1)
                        and splits selected celltypes into marker+ and
                        marker- celltypes.
