Man pages for akoyabio/phenoptr
inForm Helper Functions
| compute_all_nearest_distance | Nearest neighbors from a file. |
| count_touching_cells | Find and count touching cells for pairs of phenotypes. |
| count_touching_cells_fast | Count touching cells for a single pair of phenotypes |
| count_within | Count cells within a radius for a single field. |
| count_within_batch | Count cells within a radius for multiple tissue categories,... |
| count_within_detail | Compute count within for individual cells in a single field. |
| count_within_many | Count cells within a radius for multiple tissue categories... |
| count_within_many_impl | Helper function for count_within_batch and count_within_many.... |
| count_within_many_impl_dist | Distance matrix implementation of count_within_many_impl |
| count_within_many_impl_rtree | rtree implementation of count_within_many_impl |
| density_at_distance | Estimate cell density at distance from a tissue boundary. |
| density_bands | Estimate cell density in bands from a tissue boundary. |
| distance_matrix | Create a distance matrix from cell seg data. |
| field_column | Get the name of the column that distinguishes fields in a... |
| find_nearest_distance | Nearest neighbor distances for each cell and phenotype. |
| find_nearest_distance_dist | Distance-matrix implementation of 'find_nearest_distance'. |
| find_nearest_distance_rtree | 'rtree'-based implementation of 'find_nearest_distance'. |
| get_field_info | Read information about a field from a component image file. |
| get_map_path | Get the path to the segmentation map file for a field |
| list_cell_seg_files | Find inForm data files. |
| make_phenotype_column | Mutate a cell seg table to have a Phenotype column with the... |
| make_ppp | Make a marked point pattern for cells in a single field |
| parse_composite_info | Parse the ImageDescription of a composite image. |
| parse_names_and_colors | Parse the Entry items in a Composite or Phenotypes node |
| parse_phenotypes | Parse a vector of phenotype names |
| parse_tissue_description | Parse the description tag of the tissue map image read from... |
| phenoptr-package | Helpers for working with inForm data |
| phenotype_columns | Find the columns used by phenotype formulae |
| phenotype_names | Make user-friendly names for phenotypes |
| plot_diverging | Plot a distance map using a diverging color scale with white... |
| read_cell_seg_data | Read and clean an inForm data file. |
| read_components | Read a component TIFF file. |
| read_composite_info | Read just the composite info from images in a TIFF composite... |
| read_composites | Read composite images |
| read_field_info | Read information about a field from a component image file. |
| read_maps | Read an inForm segmentation map file. |
| readTIFFDirectory | Read directory info from a TIFF file |
| sample_cell_seg_data | Sample cell segmentation data. |
| select_rows | Flexibly select rows of a data frame. |
| spatial_distribution_report | Create a spatial distribution report. |
| split_and_trim | Split a single string and trim white space from the results |
| split_quoted | Split a single string on / and trim white space from the... |
| stop_if_multiple_fields | Stop if 'csd' contains multiple fields |
| subset_distance_matrix | Subset the rows and columns of a distance matrix. |
| unique_phenotypes | Find unique phenotypes in a cell seg table |
| validate_phenotype_definitions | Validate a user-specified phenotype definition |
| validate_phenotypes | Validate a phenotype parameter |
