fpcountr v1.0.0

New functionality

• Added ability to process single timepoint data to process_plate(), calc_fppercell() and calc_fpconc() with timecourse = FALSE argument. These produce 96-well heatmap plots in place of timecourse plots.
• Added ability to process fluorescence data without OD (cell free fluorescence data) to process_plate(). This is triggered by od_name = NULL.
• Added parsers for Tecan Spark plate reader running SparkControl software: parse_sparkcontrol() for standard/endpoint or timecourse/kinetic data, and parse_sparkcontrol_spectrum() for spectrum data.
• Added new plate formatting functions: find_wells(), find_wells_in_row(), find_wells_in_column() and find_wells_in_rowcolumn(). These enable plate reader experiment analysis using plates of any size from 6- to 384-well sizes. The functions can also be used as helpers as a shorthand for referring to all wells in a given row, e.g. for specifying blank or empty wells in process_plate(), calc_fppercell() or calc_fpconc(). They also help behind the scenes to fit plots produced by process_plate(), calc_fppercell() and calc_fpconc() to the plate size automatically.
• Added new function to generate metadata template files, save_metadata_template().

Updated functions

• Standardised function names by:
  • adopting verb-first function names, i.e. parse_[instrument_software_name](), e.g. magellan_parse() -> parse_magellan(), magellan_spectrum_parse() -> parse_magellan_spectrum()
  • clarifying others e.g. get_properties() -> get_fpbase_properties(), plot_absorbance_spectrum() -> process_absorbance_spectrum()
  • standardising them as all lowercase e.g. get_conc_A280() -> get_conc_a280(), get_conc_ECmax() -> get_conc_ecmax().
• Standardised argument names: layout_csv updated to metadata_csv in parsers and generate_cfs().
• Standardised saved file names from process_plate(), calc_fppercell() and calc_fpconc().
• Standardised plot styles in process_plate() and calc_fppercell().
• Corrected plot labels in process_plate().
• Removed hardcoded requirement in certain functions (process_absorbance_spectrum(), get_conc_ecmax(), generate_cfs()) for specific column names.
• Removed the ability of any function to silently save files. Most functions will now only save files if outfolder is specified as a valid path. Parsers only save files if save_file is set to TRUE.

Breaking changes

• Parsing functions now only save files if save_file is set to TRUE. Without this, they just return the parsed data as a dataframe.

New and updated vignettes

• The Get Started vignette has been updated for clarity. Every relevant function and argument is now explained in the plate reader data parsing-calibration-quantification workflow, along with the details of all output CSV files. Updated plots at the end to clarify information gained from calibration. Code updated to improve concentration estimation in example.
• Data Parsing and Metadata vignette explains what the data parsing functions do, and the metadata they expect. It also shows you other ways to parse your data if the package functions don't cover your plate reader.
• Path Lengths vignette describes why path length determination is important for calculating absolute concentrations from absorbance data, and the options for path length calculation within plot_absorbance_spectrum().
• Experiments I: Timecourse cellular data describes how to use the experimental data processing functions (process_data() etc.) for data collected from microbial growth-linked fluorescent protein expression.
• Experiments II: Endpoint data describes how to use the experimental data processing functions (process_data() etc.) for data collected at a single timepoint, and the different types of plots it produces.
• Experiments III: Cell-free data describes how to use the experimental data processing functions (process_data() etc.) for fluorescence data collected without OD readings (e.g. for cell-free translation or purified FP quantification).
• Plate formatting functions vignette describes the use of functions such as find_wells_in_column().

Updated documentation

• Updated package Title and Description.
• Updated README.
• Added CITATION file.
• Updated function documentation.
• Updated website to Bootstrap 5, and to include new functions in Reference list.

Minor bug fixes and improvements

• Numerous minor bug fixes.
• The OD name is now case insensitive in process_plate().
• Improved error checks in process_plate(), get_properties() and get_conc_ECmax().
• Fixed function examples in process_plate() and calc_fppercell().
• Updated parse_magellan() to follow tidyverse style code.
• Compressed image files on website to reduce package size.