Function reference • phenoptrReports

RStudio Addins These functions are added to the RStudio Addins menu. Selecting one opens a GUI.
`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 selected export folder.
`addin_50_component_levels()`	Generate a component levels report for a selected export folder.
`addin_60_mean_of_top_and_bottom_cells()`	Generate a "Mean of top and bottom cells" report for a selected merge data file and configuration file.
`addin_70_staining_consistency_report()`	Generate a "Staining consistency" report for a selected merge data file.
Merging and Consolidation These functions implement the merge and consolidation apps.
`merge_cell_seg_files()`	Merge inForm output from multiple fields.
`consolidate_and_summarize_cell_seg_data()`	Consolidate cell seg data files from parallel projects and create summary reports
Calculations These functions perform the calculations for an analysis.
`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 marker.
`compute_mean_expression_many()`	Compute mean expression of cells for multiple phenotypes and markers.
`compute_positivity()`	Compute positivity of a single phenotype
`compute_positivity_many()`	Compute positivity of multiple phenotypes
`counts_to_percents()`	Convert a count table to fractional percents
`count_phenotypes()`	Count phenotypes per slide and tissue category
`count_within_summary()`	Summarize "count within" distances
`nearest_neighbor_summary()`	Summarize nearest neighbor distances
Mean of top and bottom cells These functions implement the Mean of top 20 / bottom 10 cells report
`mean_of_top_and_bottom_cells_report()`	Create reports showing mean expression of top and bottom cells
`mean_of_top_and_bottom_cells()`	Compute mean expression levels of the top and bottom expressing cells, per Slide ID or field. This creates a quality report.
`write_mean_of_top_and_bottom_charts()`	Create summary charts from the results of `mean_of_top_and_bottom_cells`
Data reporting - HTML These functions write analysis results to HTML reports.
`component_levels_report()`	Create a component levels report for multiplex samples
`staining_consistency_report()`	Actually generate the staining consistency report
`unmixing_quality_report()`	Create an unmixing quality report for simplex samples
`write_summary_report()`	Create a summary report for a cell seg data file
Data reporting - Excel and Word These functions write analysis results to Excel worksheets and Word documents.
`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_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_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_sheet()`	Write a summary table to an Excel workbook
Helper functions
`choose_directory()`	Cross-platform choose directory function.
`choose_files()`	Cross-platform choose files function
`discrete_colors()`	Create a discrete palette with `n` colors
`nearest_neighbor_map()`	Make a nearest neighbor map for a single field
`order_by_slide_and_tissue_category()`	Order a data frame by slide ID and tissue category, putting the categories in the given order and the "Total" category in the proper place.
`spatial_map_viewer()`	Run the spatial map viewer with the given data file and export directory.
`split_phenotypes()`	Split all phenotype columns
`unmixing_quality_report()`	Create an unmixing quality report for simplex samples
`upset_plot()`	Create an UpSet plot showing the phenotype combinations present in data.
`write_session_info()`	Write session info to a file

Reference

RStudio Addins

Merging and Consolidation

Calculations

Mean of top and bottom cells

Data reporting - HTML

Data reporting - Excel and Word

Helper functions