Man pages for akoyabio/phenoptrReports
Create reports using Phenoptics data
| addin_10_merge | Merge cell seg data files |
| addin_20_consolidate | Consolidate and summarize cell seg data files |
| addin_30_analysis_app | Run the Analysis app |
| addin_35_spatial_map_viewer | Spatial map viewer addin |
| addin_40_unmixing_quality | Generate an unmixing quality (crosstalk) report for a... |
| addin_50_component_levels | Generate a component levels report for a selected export... |
| addin_60_mean_of_top_and_bottom_cells | Generate a "Mean of top and bottom cells" report for a... |
| addin_70_staining_consistency_report | Generate a "Staining consistency" report for a selected merge... |
| choose_directory | Cross-platform choose directory function. |
| choose_files | Cross-platform choose files function |
| component_levels_report | Create a component levels report for multiplex samples |
| compute_density_from_cell_summary | Compute cell densities from counts and tissue area |
| compute_density_from_table | Compute cell densities from counts and tissue area |
| compute_h_score | Compute H-Score for a single marker aggregated by '.by' |
| compute_h_score_from_score_data | Compute H-Score based on parameters in a score data file |
| compute_mean_expression | Compute mean expression of cells for a single phenotype and... |
| compute_mean_expression_many | Compute mean expression of cells for multiple phenotypes and... |
| compute_positivity | Compute positivity of a single phenotype |
| compute_positivity_many | Compute positivity of multiple phenotypes |
| consolidate_and_summarize_cell_seg_data | Consolidate cell seg data files from parallel projects and... |
| count_phenotypes | Count phenotypes per slide and tissue category |
| counts_to_percents | Convert a count table to fractional percents |
| count_within_summary | Summarize "count within" distances |
| discrete_colors | Create a discrete palette with 'n' colors |
| mean_of_top_and_bottom_cells | Compute mean expression levels of the top and bottom... |
| mean_of_top_and_bottom_cells_report | Create reports showing mean expression of top and bottom... |
| merge_cell_seg_files | Merge inForm output from multiple fields. |
| nearest_neighbor_map | Make a nearest neighbor map for a single field |
| nearest_neighbor_summary | Summarize nearest neighbor distances |
| order_by_slide_and_tissue_category | Order a data frame by slide ID and tissue category, putting... |
| spatial_map_viewer | Run the spatial map viewer with the given data file and... |
| split_phenotype_column | Split a single phenotype column |
| split_phenotypes | Split all phenotype columns |
| staining_consistency_report | Actually generate the staining consistency report |
| unmixing_quality_report | Create an unmixing quality report for simplex samples |
| upset_plot | Create an UpSet plot showing the phenotype combinations... |
| write_counts_sheet | Write a cell counts table to an Excel workbook |
| write_count_within_sheet | Write a "count within" summary to an Excel workbook |
| write_density_sheet | Write a density table to an Excel workbook |
| write_expression_sheet | Write an expression table to an Excel workbook |
| write_h_score_sheet | Write an H-Score table to an Excel workbook |
| write_mean_of_top_and_bottom_charts | Create summary charts from the results of... |
| write_nearest_neighbor_summary_sheet | Write a nearest neighbor summary to an Excel workbook |
| write_percents_sheet | Write a cell percent table to an Excel workbook |
| write_plot_sheet | Write a plot to an Excel workbook |
| write_session_info | Write session info to a file |
| write_sheet | Write a single sheet with formatting common to all sheets. |
| write_summary_charts | Create summary charts from the results of an analysis |
| write_summary_report | Create a summary report for a cell seg data file |
| write_summary_sheet | Write a summary table to an Excel workbook |
