README.md
In akoyabio/phenoptrReports: Create reports using Phenoptics data

phenoptrReports

phenoptrReports generates reports and visualizations based on data created by Akoya Biosciences' inForm® software.

phenoptrReports is part of the Akoya Biosciences Phenoptics™ family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.

The analysis apps in phenoptrReports run as "Addins" to the RStudio IDE, which must also be installed.

phenoptrReports uses the Akoya Biosciences phenoptr package for much of its functionality. Please follow the phenoptr installation instructions, including the optional installations, before installing phenoptrReports.

Next, install phenoptrReports from GitHub. In the RStudio console, copy and paste or type this command:

remotes::install_github("akoyabio/phenoptrReports")

phenoptrReports functionality is provided via RStudio Addins. These are small applications accessed via the "Addins" menu in the RStudio IDE.

The Merge cell seg files addin merges inForm data files from individual fields to create "Merge" data files. This is similar to the inForm Merge tab but does not include the ability to review and reject individual fields. Use this addin if you are not able to merge in inForm for any reason.

This addin allows you to select an inForm export directory containing data files for individual fields. It creates merge data files combining data for all fields.

The Consolidate and summarize addin combines the output from multiple inForm projects into a single consolidated data file, creating columns for each individual phenotype. The inputs to this addin are merged cell seg data files created by inForm. The output is a consolidated data file and a summary report for each file.

Run the consolidation addin even if your data comes from a single inForm project. This creates a data file in the format that the analysis addin uses.

For detailed instructions and requirements, see the Consolidating inForm data tutorial.

The Analyze consolidated data addin reads data produced by the consolidation addin. It aggregates phenoype counts, density, mean expression and H-Score for each slide and tissue category in an experiment and can also report on nearest neighbors and count cells within a radius.

This addin creates

an Excel workbook with aggregation results
a Word document with visualizations of the results
CSV files containing spatial metrics
an R script which provides an audit trail and can be used to reproduce or modify the analysis.

The analysis addin has three parts:

select the input files
define the desired analysis
create the final reports

The most important input file is the consolidated data file from the consolidation addin. Selecting a summary cell seg data file enables density calculations; selecting a score data file enables H-Score calculation.

To define the analysis, you select tissue categories, phenotypes, and markers of interest.

To create the final reports, the analysis app writes and runs an R script. The script computes the aggregated statistics, writes them to an Excel workbook, and creates visualizations of the results in a Word document.

For detailed instructions and requirements, see the Analyzing inForm data tutorial.

The Spatial map viewer addin creates visualizations of nearest neighbors of selected phenotypes within individual fields. The visualizations can be saved for use in other applications.

The spatial map viewer requires a Consolidated_data.txt file from the consolidation app or the nearest_neighbors.csv file created by the analysis addin, and an inForm image directory containing composite and component images.

For detailed instructions and requirements, see the Visualizing spatial relationships tutorial.

The Unmixing quality report addin analyzes unmixed, singleplex images to help evaluate staining and unmixing quality. This report shows crosstalk between components and highlights potential problem areas in assay development.

For more information about the unmixing quality report, see the Unmixing quality report tutorial.

The Component levels report addin analyzes unmixed, multiplex images to help evaluate staining levels for an entire experiment. This report shows the distribution of signal and dark pixels for all components.

For more information about the component levels report, see the Component levels report tutorial.

The Mean of Top 20/ bottom 10 analysis helps to evaluate whether the staining quality is likely to produce good unmixing of the markers in the image. The analysis computes the mean expression of selected markers in the 20 highest-expressing cells and the 10% lowest-expressing cells.

For detailed instructions and requirements, see the Mean of top 20 / bottom 10 cells tutorial.

The Staining consistency report measures variation in the mean expression of a single marker across multiple images. It is used to assess consistency of staining across multiple staining runs.

For detailed instructions and requirements, see the Staining consistency report tutorial.