A package to extract spatial features based on multiplex IF images


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Documentation for package ‘IrisSpatialFeatures’ version 1.3.0

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IrisSpatialFeatures-package IrisSpatialFeatures: A package to extract spatial features based on multiplex IF images
as.data.frame-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
collapse_markers-method 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
Coordinate Class to represent a single imaging coordinate
Coordinate-class Class to represent a single imaging coordinate
extract.nearest.neighbor-method Extract the distance to each nearest neighbor for each cell-type
extract_features Extract all spatial features
extract_features-method Extract all spatial features
extract_interactions Extract interactions between all cell-types
extract_interactions-method 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_nearest_neighbor-method 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.
extract_proximity-method 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.
extract_ROI Method that reduces the current dataset to a specific region of interest, discarding all cell coordinates outside of that region
extract_ROI-method Method that reduces the current dataset to a specific region of interest, discarding all cell coordinates outside of that region
feature_selection Function to extract all numeric features
get_all_interactions Get all interactions between all cell-types
get_all_interactions-method Get all interactions between all cell-types
get_all_nearest_neighbors Get the nearest neighbor for each cell-type
get_all_nearest_neighbors-method Get the nearest neighbor for each cell-type
get_all_proximities Get all proximity data for all cell-types in a sample
get_all_proximities-method Get all proximity data for all cell-types in a sample
get_counts_per_mm2 Get all the counts on a per mm2 basis
get_counts_per_mm2-method 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_counts_per_mm2_noncollapsed-method Get all the counts on a per mm2 basis non-collapsed
get_count_ratios Get ratio of counts between two markers
get_count_ratios-method Get ratio of counts between two markers
get_interactions Get interactions for a specific marker
get_interactions-method Get interactions for a specific marker
get_nearest_neighbors Get the nearest neighbor for a specified cell-type
get_nearest_neighbors-method Get the nearest neighbor for a specified cell-type
get_proximities Get proximity data for a given cell-type
get_proximities-method Get proximity data for a given cell-type
ImageSet Class to represent an imaging dataset.
ImageSet-class Class to represent an imaging dataset.
interaction_maps Plot interaction maps for all samples
interaction_maps-method Plot interaction maps for all samples
IrisSpatialFeatures IrisSpatialFeatures: A package to extract spatial features based on multiplex IF images
IrisSpatialFeatures_data Example IrisSpatialFeatures dataset
neighbor.ray.plot-method Plot nearest neighbor ray plots for each samples
neighbor_ray_plot Plot nearest neighbor ray plots for each samples
neighbor_ray_plot-method Plot nearest neighbor ray plots for each samples
overview_plot Plot all coordinates in a given dataset
overview_plot-method Plot all coordinates in a given dataset
plot-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_interactions-method 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_nearest_neighbor-method 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
plot_proximities-method Plot proximity analysis data
raw_data Class to represent the raw data that is output by inForm
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
rayplot_single_coordinate-method Plot nearest neighbor ray plots for a single coordinate
read_raw Read inForm output and store it in an IrisSpatialFeatures ImageSet object.
read_raw-method Read inForm output and store it in an IrisSpatialFeatures ImageSet object.
run_proximity-method 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.
Sample An S3 class to represent a single imaging sample with multiple coordinates.
Sample-class An S3 class to represent a single imaging sample with multiple coordinates.
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.
threshold_dataset-method This function reads the manually determined thresholds of certain markers (e.g. PD1, PD-L1) and splits selected celltypes into marker+ and marker- celltypes.