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. |