CalFluxTools

CalFluxTools is an R package for parsing, quality-controlling, visualizing, transforming, and analyzing calcium flux plate-reader data. It currently is designed for ScreenWorks-normalized data from the FLIPR platform in statAll format.

For a worked example, see the CalFluxTools example-data vignette.

Installation

remotes::install_github("ncats/CalFluxTools")

Quick start

Once a correctly formatted parameter manifest and its referenced data files are in place, the complete workflow is run with one line of code:

calflux_data <- CalFluxTools::processCalFluxData("path/to/parameter_manifest.xlsx")

See the vignette for an example of a correctly formatted parameter manifest. The manifest identifies the input files, plate maps, plate layout, output organization, parameters to retain, processing rules, and analyses to run. processCalFluxData() uses those settings to load and organize the data, run the configured workflow, write reports and figures, and return a CalFluxData object containing the processed data and analysis results.

Input files

A typical analysis uses:

• an Excel parameter manifest containing Analysis_Settings and Parameter_Info worksheets;
• one or more ScreenWorks-normalized statAll files; and
• CSV plate maps containing well-level sample annotations.

The filenames and locations of the data and plate maps are specified in the manifest. Example manifests, plate maps, and statAll files are provided under inst/extdata.

Workflow and outputs

Depending on the manifest settings, CalFluxTools can:

• parse plate-reader data and attach well annotations;
• mask unused wells and handle blank or missing values;
• filter parameters and encode categorical measurements;
• transform paired plate reads relative to baseline;
• assess data completeness and reference-plate quality;
• generate plate views, heatmaps, bar charts, and z-prime summaries;
• run t-tests and principal component analysis; and
• run random-forest classification and export prediction summaries.

Reports, plots, spreadsheets, and logs are written beneath the configured root directory. The returned CalFluxData object can also be used with exported lower-level functions for custom exploration and analysis.

Example workflow

The example-data vignette demonstrates the package with the data included in this repository. It covers the manifest-driven wrapper as well as lower-level parsing, quality-control, transformation, and visualization functions.

License

CalFluxTools is distributed under the GPL-2 license. See LICENSE for details.