A vector of concentration values

The minimum fluorescence value

The maximum fluorescence value

Sensitivity parameter

Cooperativity parameter

The text for the tooltip's title.

Placement of the tooltip. One of 'top', 'bottom', 'left', or 'right'.

The events that trigger the tooltip. One or more of 'click', 'hover', 'focus', or 'manual'.

A list of additional options for the tooltip.

Optional HTML content for the tooltip.

An R object.

The path to the output directory. Default: the working directory

The output filename (with or without '.RData' ending). Default: the class of object followed by '.RData'.

A tabular R object (dataframe, matrix, array)

The path to the output directory. Default: the working directory

The output filename (with or without '.txt' ending). Default: the name of table followed by '.txt'.

(Character or vector of strings) Indicates whether the program should perform a linear regression ('l') and/or spline fit ('s'). Default: fit.opt = c('l', 's').

(Character) Which data type shall be used as independent variable? Options are 'growth' and 'time'.

(Logical) use normalized (to growth) fluorescence data in fits. Has an effect only when x_type = 'time'

(Numeric) Minimum time value considered for linear and spline fits (if x_type = 'time').

(Numeric) Maximum time value considered for linear and spline fits (if x_type = 'time')..

(Numeric) Indicate whether only values above a certain threshold should be considered for linear regressions or spline fits (if x_type = 'growth').

(Numeric) Indicate whether only growth values below a certain threshold should be considered for linear regressions or spline fits (if x_type = 'growth').

(Logical) Indicates whether ln(x+1) should be applied to the independent variable for linear fits. Default: FALSE.

(Logical) Indicates whether ln(x+1) should be applied to the independent variable for spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the fluorescence data for linear fits. Default: FALSE

(Logical) Indicates whether ln(y/y0) should be applied to the fluorescence data for spline fits. Default: FALSE

(Numeric) Manually define the size of the sliding window used in flFitLinear. If NULL, h is calculated for each samples based on the number of measurements in the fluorescence increase phase of the plot.

(Numeric) R² threshold for flFitLinear.

(Numeric) Relative standard deviation (RSD) threshold for the calculated slope in flFitLinear.

(Numeric) Threshold for the minimum fraction of growth increase a linear regression window should cover. Default: 0.05 (5%).

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See fl.drFit for further details. Default: 'max_slope.spline', which represents the maximum slope of the spline fit Typical options include: 'max_slope.linfit', 'dY.linfit', 'max_slope.spline', and 'dY.spline'.

(Character) Perform either a smooth spline fit on response parameter vs. concentration data ('spline') or fit a biosensor response model with 'model' (proposed by Meyer et al., 2019).

(Numeric) Minimum number of different values for the response parameter one should have for estimating a dose response curve. Note: All fit procedures require at least six unique values. Default: 6.

(Numeric) Smoothing parameter used in the spline fit by smooth.spline during dose response curve estimation. Usually (not necessesary) in (0; 1]. See smooth.spline for further details. Default: NULL.

(Logical) Indicates whether ln(x+1) should be applied to the concentration data of the dose response curves. Default: FALSE.

(Logical) Indicates whether ln(y+1) should be applied to the response data of the dose response curves. Default: FALSE.

(Numeric) Defines the number of bootstrap samples for EC50 estimation. Use nboot.dr = 0 to disable bootstrapping. Default: 0.

(Logical) Shall flFitLinear and flFitSpline try to extract fluorescence parameters for two different phases (as observed with, e.g., regulator-promoter systems with varying response in different growth stages) (TRUE) or not (FALSE)?

(Logical) Controls whether the fit for each sample and method is controlled manually by the user. If TRUE, each fit is visualized in the Plots pane and the user can adjust fitting parameters and confirm the reliability of each fit per sample. Default: TRUE.

(Numeric) Number of bootstrap samples used for nonparametric curve fitting with flBootSpline. Use nboot.fl = 0 to disable the bootstrap. Default: 0

(Numeric) Parameter describing the smoothness of the spline fit; usually (not necessary) within (0;1]. smooth.gc=NULL causes the program to query an optimal value via cross validation techniques. Especially for datasets with few data points the option NULL might cause a too small smoothing parameter. This can result a too tight fit that is susceptible to measurement errors (thus overestimating slopes) or produce an error in smooth.spline or lead to overfitting. The usage of a fixed value is recommended for reproducible results across samples. See smooth.spline for further details. Default: 0.55

(Numeric) Define a threshold for growth. Only if any growth value in a sample is greater than growth.thresh (default: 1.5) times the start growth, further computations are performed. Else, a message is returned.

(Logical) Indicates whether messages (information about current fluorescence curve, EC50 values etc.) should be displayed (FALSE) or not (TRUE). This option is meant to speed up the high-throughput processing data. Note: warnings are still displayed. Default: FALSE.

(Logical) Indicates whether the program should stop when negative fluorescence values or NA values appear (TRUE). Otherwise, the program removes these values silently (FALSE). Improper values may be caused by incorrect data or input errors. Default: FALSE.

(Logical) Determines if negative values which occur during bootstrap should be removed (TRUE) or kept (FALSE). Note: Infinite values are always removed. Default: TRUE.

A dataframe containing the data for the dose-response model estimation. Such table of class flTable can be obtained by running flFit with dr.method = 'model' as argument in the fl.control object.

A fl.control object created with fl.control, defining relevant fitting options.

(Character) Perform either a smooth spline fit on response parameter vs. concentration data ('spline') or fit a biosensor response model with 'model' (proposed by Meyer et al., 2019).

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See fl.drFit for further details. Default: 'max_slope.spline', which represents the maximum slope of the spline fit Typical options include: 'max_slope.linfit', 'dY.linfit', 'max_slope.spline', and 'dY.spline'.

Data that passed to the function as flTable.

Dataframe containing condition identifiers, fit options, and results of the dose-response analysis.

List of all drFitModel objects generated by the call of fl.drFitModel for each distinct experiment.

Object of class fl.control created with the call of fl.control.

Vector of concentration values.

Vector of response parameter values of the same length as conc.

(Character) The name of the analyzed condition

A fl.control object created with fl.control, defining relevant fitting options.

Raw data provided to the function as conc.

Raw data for the response parameter provided to the function as test.

(Character) Identifies the tested condition

Fitted concentration values.

Fitted response values.

nls object generated by the nlsLM function.

List of parameters estimated from dose response curve fit.

(Logical) Indicates whether a spline could fitted successfully to data.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

Object of class fl.control created with the call of fl.control.

A grofit object created with fl.workflow.

(Character) The path or name of the folder in which the report files are created. If NULL, the folder will be named with a combination of 'Report.fluorescence_' and the current date and time.

Character or NULL Define the name of the report files. If NULL, the files will be named with a combination of 'FluorescenceReport_' and the current date and time.

(Logical) Display results of dose-response analysis (TRUE) or not (FALSE).

(Character) Define the file format for the report, PDF ('pdf') and/or HTML ('html'). Default: (c('pdf', 'html'))

(Logical) Shall all plots generated in the report be exported as individual PDF and PNG files TRUE or not FALSE?

(Logical) Create plots using all but one available processor cores (TRUE) or only a single core (FALSE).

Further arguments passed to create a report. Currently supported:

• mean.grp: Define groups to combine into common plots in the report based on sample identifiers. Partial matches with sample/group names are accepted. Can be 'all', a vector of strings, or a list of string vectors. Note: The maximum number of sample groups (with unique condition/concentration indicators) is 50. If you have more than 50 groups, option 'all' will produce the error ! Insufficient values in manual scale. [Number] needed but only 50 provided.

• mean.conc: Define concentrations to combine into common plots in the report. Can be a numeric vector, or a list of numeric vectors.

A grodata object created with read_data or parse_data, containing fluorescence data and data for the independent variable (i.e., time or growth).

(optional) A matrix containing time values for each sample (if a fl_data dataframe is provided as separate argument).

(optional) A dataframe containing growth data (if a fl_data matrix is provided as separate argument).

(optional) A dataframe containing fluorescence data (if a time matrix or growth dataframe is provided as separate argument).

(Logical) Perform dose-response analysis (TRUE) or not (FALSE).

("all", a string vector, or a list of string vectors) Define groups to combine into common plots in the final report based on sample identifiers (if report == TRUE). Partial matches with sample/group names are accepted. Note: The maximum number of sample groups (with unique condition/concentration indicators) is 50. If you have more than 50 groups, option "all" will produce the error ! Insufficient values in manual scale. [Number] needed but only 50 provided.

(A numeric vector, or a list of numeric vectors) Define concentrations to combine into common plots in the final report (if report == TRUE).

(Character or character vector) Indicates whether the program should perform a linear regression ("l"), model fit ("m"), spline fit ("s"), or all ("a"). Combinations can be freely chosen by providing a character vector, e.g. fit.opt = c("l", "s") Default: fit.opt = c("l", "s").

(Character) Which data type shall be used as independent variable? Options are 'growth' and 'time'.

(Logical) use normalized (to growth) fluorescence data in fits. Has an effect only when x_type = 'time'

(Numeric) Minimum time value considered for linear and spline fits (if x_type = 'time').

(Numeric) Maximum time value considered for linear and spline fits (if x_type = 'time')..

(Numeric) Indicate whether only values above a certain threshold should be considered for linear regressions or spline fits (if x_type = 'growth').

(Numeric) Indicate whether only growth values below a certain threshold should be considered for linear regressions or spline fits (if x_type = 'growth').

(Logical) Indicates whether ln(x+1) should be applied to the independent variable for linear fits. Default: FALSE.

(Logical) Indicates whether ln(x+1) should be applied to the independent variable for spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the fluorescence data for linear fits. Default: FALSE

(Logical) Indicates whether ln(y/y0) should be applied to the fluorescence data for spline fits. Default: FALSE

(Numeric) Manually define the size of the sliding window used in flFitLinear. If NULL, h is calculated for each samples based on the number of measurements in the fluorescence increase phase of the plot.

(Numeric) R² threshold for flFitLinear.

(Numeric) Relative standard deviation (RSD) threshold for the calculated slope in flFitLinear.

(Numeric) Threshold for the minimum fraction of growth increase a linear regression window should cover. Default: 0.05 (5%).

(Logical) Shall flFitLinear and flFitSpline try to extract fluorescence parameters for two different phases (as observed with, e.g., regulator-promoter systems with varying response in different growth stages) (TRUE) or not (FALSE)?

(Logical) Controls whether the fit for each sample and method is controlled manually by the user. If TRUE, each fit is visualized in the Plots pane and the user can adjust fitting parameters and confirm the reliability of each fit per sample. Default: TRUE.

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See fl.drFit for further details. Default: "max_slope.spline", which represents the maximum slope of the spline fit Typical options include: "max_slope.linfit", "dY.linfit", "max_slope.spline", and "dY.spline".

(Character) Perform either a smooth spline fit on response parameter vs. concentration data ("spline") or fit a biosensor response model (proposed by Meyer et al., 2019).

(Numeric) Minimum number of different values for the response parameter one should have for estimating a dose response curve. Note: All fit procedures require at least six unique values. Default: 6.

(Numeric) Smoothing parameter used in the spline fit by smooth.spline during dose response curve estimation. Usually (not necessesary) in (0; 1]. See smooth.spline for further details. Default: NULL.

(Logical) Indicates whether ln(x+1) should be applied to the concentration data of the dose response curves. Default: FALSE.

(Logical) Indicates whether ln(y+1) should be applied to the response data of the dose response curves. Default: FALSE.

(Numeric) Defines the number of bootstrap samples for EC50 estimation. Use nboot.dr = 0 to disable bootstrapping. Default: 0.

(Numeric) Number of bootstrap samples used for nonparametric curve fitting with flBootSpline. Use nboot.fl = 0 to disable the bootstrap. Default: 0

(Numeric) Parameter describing the smoothness of the spline fit; usually (not necessary) within (0;1]. smooth.gc=NULL causes the program to query an optimal value via cross validation techniques. Especially for datasets with few data points the option NULL might cause a too small smoothing parameter. This can result a too tight fit that is susceptible to measurement errors (thus overestimating slopes) or produce an error in smooth.spline or lead to overfitting. The usage of a fixed value is recommended for reproducible results across samples. See smooth.spline for further details. Default: 0.55

(Numeric) Define a threshold for growth. Only if any growth value in a sample is greater than growth.thresh (default: 1.5) times the start growth, further computations are performed. Else, a message is returned.

(Logical) Indicates whether messages (information about current fluorescence curve, EC50 values etc.) should be displayed (FALSE) or not (TRUE). This option is meant to speed up the high-throughput processing data. Note: warnings are still displayed. Default: FALSE.

(Logical) Indicates whether the program should stop when negative fluorescence values or NA values appear (TRUE). Otherwise, the program removes these values silently (FALSE). Improper values may be caused by incorrect data or input errors. Default: FALSE.

(Logical) Determines if negative values which occur during bootstrap should be removed (TRUE) or kept (FALSE). Note: Infinite values are always removed. Default: TRUE.

(Character or NULL) Create a PDF ('pdf') and/or HTML ('html') report after running all computations. Define NULL if no report should be created. Default: (c('pdf', 'html'))

Character or NULL Define the name of a folder in which all result files (tables and reports) are stored. If NULL, the folder will be named with a combination of "FluorescenceResults_" and the current date and time.

Character or NULL Define the name of the report files. If NULL, the files will be named with a combination of "FluorescenceReport_" and the current date and time.

(Logical) Export all figures created in the report as separate PNG and PDF files (TRUE) or not (FALSE). Only effective if report = TRUE.

(Logical) Create tab-separated TXT files containing calculated parameters and dose-response analysis results as well as an .RData file for the resulting flFitRes object.

Run linear fits and bootstrapping operations in parallel using all but one available processor cores

Further arguments passed to the shiny app.

Raw time matrix passed to the function as time (if no grofit object is provided. Else, extracted from grofit).

Raw data dataframe passed to the function as grodata.

flFit object created with the call of flFit on fluorescence data.

drFit or drFitfl object created with the call of growth.drFit or fl.drFit for fluorescence data (based on the dr.method argument in control; see fl.control).

Experimental design table inherited from grodata or created from the identifier columns (columns 1-3) in data.

Object of class fl.control created with the call of fl.control.

Vector of the independent variable: time (if x_type = 'time' in fl.control object.

Vector of the independent variable: growth (if x_type = 'growth' in fl.control object.

Vector of dependent variable: fluorescence.

(Character) The name of the analyzed sample.

A fl.control object created with fl.control, defining relevant fitting options.

Raw time values provided to the function as time.

Raw growth data provided to the function as data.

(Character) Identifies the tested sample.

Table of time values per column, resulting from each spline fit of the bootstrap.

Table of growth values per column, resulting from each spline fit of the bootstrap.

List of flFitSpline object, created by flFitSpline for each resample of the bootstrap.

Vector of estimated lambda (lag time) values from each bootstrap entry.

Vector of estimated max_slope (maximum slope) values from each bootstrap entry.

Vector of estimated A (maximum fluorescence) values from each bootstrap entry.

Vector of estimated integral values from each bootstrap entry.

(Logical) Indicates the success of the bootstrapping operation.

Object of class fl.control containing list of options passed to the function as control.

Either...

1. a grodata object created with read_data or parse_data,

2. a list containing a 'time' matrix (for x_type == "time") or 'growth' dataframe (for x_type == "growth") and a 'fluorescence' dataframes, or

3. a dataframe containing (normalized) fluorescence values (if a time matrix or growth dataframe is provided as separate argument).

(optional) A matrix containing time values for each sample.

(optional) A dataframe containing growth values for each sample and sample identifiers in the first three columns.

A fl.control object created with fl.control, defining relevant fitting options.

Run linear fits and bootstrapping operations in parallel using all but one available processor cores

Further arguments passed to the shiny app.

Raw x matrix passed to the function as time (for x_type = 'time') or growth (for x_type = 'growth').

Raw growth dataframe passed to the function as data.

Table with fluorescence parameters and related statistics for each fluorescence curve evaluation performed by the function. This table, which is also returned by the generic summary.flFit method applied to a flFit object, is used as an input for fl.drFit.

List of all flFitLinear objects, generated by the call of flFitLinear. Note: access to each object in the list via double brace: flFittedLinear[[#n]].

List of all flFitSpline objects, generated by the call of flFitSpline. Note: access to each object via double brace: flFittedSplines[[#n]].

List of all flBootSpline objects, generated by the call of flBootSpline. Note: access to each object via double brace: flFittedSplines[[#n]].

Object of class fl.control containing list of options passed to the function as control.

Vector of the independent time variable (if x_type = "time" in control object).

Vector of the independent time growth (if x_type = "growth" in control object).

Vector of the dependent fluorescence variable.

(Character) The name of the analyzed sample.

(Numeric, between 0 an 1) Define what fraction of max_slope the slope of regression windows adjacent to the window with highest slope should have to be included in the overall linear fit.

A fl.control object created with fl.control, defining relevant fitting options.

Filtered x values used for the spline fit.

Filtered fluorescence values used for the spline fit.

Filtered x values.

Filtered fluorescence values.

(Character) Identifies the tested sample.

Linear function used for plotting the tangent at mumax.

lm object; result of the final call of lm to perform the linear regression.

List of determined fluorescence parameters:

Index of data points used for the linear regression.

Index of data points used for the linear regression for the second phase.

Object of class grofit.control containing list of options passed to the function as control.

of the linear regression.

of the linear regression for the second phase.

(Logical) Indicates whether linear regression was successfully performed on the data.

(Logical) Indicates whether a second phase was identified.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

Vector of the independent variable: time (if x_type = 'time' in fl.control object.

Vector of the independent variable: growth (if x_type = 'growth' in fl.control object.

Vector of dependent variable: fluorescence.

(Character) The name of the analyzed sample.

A fl.control object created with fl.control, defining relevant fitting options.

(Logical) Shall flFitLinear and flFitSpline try to extract fluorescence parameters for two different phases (as observed with, e.g., regulator-promoter systems with varying response in different growth stages) (TRUE) or not (FALSE)?

(Character) Which data type shall be used as independent variable? Options are 'growth' and 'time'.

(Logical) Indicates whether ln(x+1) should be applied to the independent variable for spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the fluorescence data for spline fits. Default: FALSE

(Numeric) Parameter describing the smoothness of the spline fit; usually (not necessary) within (0;1]. smooth.gc=NULL causes the program to query an optimal value via cross validation techniques. Especially for datasets with few data points the option NULL might cause a too small smoothing parameter. This can result a too tight fit that is susceptible to measurement errors (thus overestimating slopes) or produce an error in smooth.spline or lead to overfitting. The usage of a fixed value is recommended for reproducible results across samples. See smooth.spline for further details. Default: 0.55

(Numeric) Minimum time value considered for linear and spline fits.

(Numeric) Indicate whether only values above a certain threshold should be considered for linear regressions or spline fits.

Raw x values provided to the function as time or growth.

Raw fluorescence data provided to the function as fl_data.

Filtered x values used for the spline fit.

Filtered fluorescence values used for the spline fit.

(Character) Identifies the tested sample.

Fitted x values.

Fitted fluorescence values.

List of determined parameters.

smooth.spline object generated by the smooth.spline function.

list of time ('x') and growth ('y') values describing the first derivative of the spline fit.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

(Logical) Indicates whether a spline fit was successfully performed on the data.

(Logical) Indicates whether a second phase was identified.

Object of class fl.control containing list of options passed to the function as control.

(Logical) Indicates whether the program should stop when negative growth values or NA values appear (TRUE). Otherwise, the program removes these values silently (FALSE). Improper values may be caused by incorrect data or input errors. Default: FALSE.

(Logical) Determines if negative values which occur during bootstrap should be removed (TRUE) or kept (FALSE). Note: Infinite values are always removed. Default: TRUE.

(Logical) Indicates whether messages (information about current growth curve, EC50 values etc.) should be displayed (FALSE) or not (TRUE). This option is meant to speed up the processing of high throughput data. Note: warnings are still displayed. Default: FALSE.

(Character or character vector) Indicates whether the program should perform a linear regression ('l'), model fit ('m'), spline fit ('s'), or all ('a'). Combinations can be freely chosen by providing a character vector, e.g. fit.opt = c('l', 's') Default: fit.opt = c('l', 's').

(Numeric) Minimum time value considered for linear and spline fits.

(Numeric) Maximum time value considered for linear and spline fits.

(Numeric) Indicate whether only growth values above a certain threshold should be considered for linear regressions or spline fits.

(Numeric) Indicate whether only growth values below a certain threshold should be considered for linear regressions or spline fits.

(Logical) Indicates whether ln(x+1) should be applied to the time data for linear and spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for linear fits. Default: TRUE

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for spline fits. Default: TRUE

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for model fits. Default: TRUE

(Numeric) Manually define the size of the sliding window used in growth.gcFitLinear If NULL, h is calculated for each samples based on the number of measurements in the growth phase of the plot.

(Numeric) R² threshold for growth.gcFitLinear

(Numeric) Relative standard deviation (RSD) threshold for the calculated slope in growth.gcFitLinear

(Numeric) Threshold for the minimum fraction of growth increase a linear regression window should cover. Default: 0.05 (5%).

(Logical) Shall growth.gcFitLinear and growth.gcFitSpline try to extract growth parameters for two different growth phases (as observed with, e.g., diauxic shifts) (TRUE) or not (FALSE)?

(Logical) Controls whether the fit of each growth curve and method is controlled manually by the user. If TRUE, each fit is visualized in the Plots pane and the user can adjust fitting parameters and confirm the reliability of each fit per sample. Default: TRUE.

(Numeric) Number of bootstrap samples used for nonparametric growth curve fitting with growth.gcBootSpline. Use nboot.gc = 0 to disable the bootstrap. Default: 0

(Numeric) Parameter describing the smoothness of the spline fit; usually (not necessary) within (0;1]. smooth.gc=NULL causes the program to query an optimal value via cross validation techniques. Especially for datasets with few data points the option NULL might cause a too small smoothing parameter. This can result a too tight fit that is susceptible to measurement errors (thus overestimating growth rates) or produce an error in smooth.spline or lead to overfitting. The usage of a fixed value is recommended for reproducible results across samples. See smooth.spline for further details. Default: 0.55

(Character) Vector providing the names of the parametric models which should be fitted to the data. Default: c('logistic', 'richards', 'gompertz', 'gompertz.exp', 'huang', 'baranyi').

(Character) Define the method used to perform a dose-responde analysis: smooth spline fit ('spline') or model fitting ('model').

(Character) Provide a list of models from the R package 'drc' to include in the dose-response analysis (if dr.method = 'model'). If more than one model is provided, the best-fitting model will be chosen based on the Akaike Information Criterion.

(Numeric) Minimum number of different values for the response parameter one should have for estimating a dose response curve. Note: All fit procedures require at least six unique values. Default: 6.

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See growth.drFit for further details. Default: 'mu.linfit', which represents the maximum slope of the linear regression. Typical options include: 'mu.linfit', 'lambda.linfit', 'dY.linfit', 'mu.spline', 'dY.spline', 'mu.model', and 'A.model'.

(Numeric) Smoothing parameter used in the spline fit by smooth.spline during dose response curve estimation. Usually (not necessesary) in (0; 1]. See smooth.spline for further details. Default: NULL.

(Logical) Indicates whether ln(x+1) should be applied to the concentration data of the dose response curves. Default: FALSE.

(Logical) Indicates whether ln(y+1) should be applied to the response data of the dose response curves. Default: FALSE.

(Numeric) Defines the number of bootstrap samples for EC50 estimation. Use nboot.dr = 0 to disable bootstrapping. Default: 0.

(Numeric) Define a threshold for growth. Only if any growth value in a sample is greater than growth.thresh (default: 1.5) times the start growth, further computations are performed. Else, a message is returned.

Vector of concentration values.

Vector of response parameter values of the same length as conc.

(Character) The name of the analyzed sample.

A grofit.control object created with growth.control, defining relevant fitting options.

Raw data provided to the function as conc.

Raw data for the response parameter provided to the function as test.

(Character) Identifies the tested condition.

Table of concentration values per column, resulting from each spline fit of the bootstrap.

Table of response values per column, resulting from each spline fit of the bootstrap.

List containing all drFitSpline objects generated by the call of growth.drFitSpline.

Vector of estimated EC50 values from each bootstrap entry.

Vector of estimated response at EC50 values from each bootstrap entry.

(Logical) Indicates the success of the bootstrapping operation.

Object of class grofit.control containing list of options passed to the function as control.

A dataframe containing the data for the dose-response curve estimation. Such table of class gcTable can be obtained by running growth.gcFit.

A grofit.control object created with growth.control, defining relevant fitting options.

(Character) Define the method used to perform a dose-responde analysis: smooth spline fit ('spline') or model fitting ('model').

(Character) Provide a list of models from the R package 'drc' to include in the dose-response analysis (if dr.method = 'model'). If more than one model is provided, the best-fitting model will be chosen based on the Akaike Information Criterion.

(Numeric) Minimum number of different values for the response parameter one should have for estimating a dose response curve. Note: All fit procedures require at least six unique values. Default: 6.

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See growth.drFit for further details. Default: 'mu.linfit', which represents the maximum slope of the linear regression. Typical options include: 'mu.linfit', 'lambda.linfit', 'dY.linfit', 'mu.spline', 'dY.spline', 'mu.model', and 'A.model'.

(Numeric) Smoothing parameter used in the spline fit by smooth.spline during dose response curve estimation. Usually (not necessesary) in (0; 1]. See smooth.spline for further details. Default: NULL.

(Logical) Indicates whether ln(x+1) should be applied to the concentration data of the dose response curves. Default: FALSE.

(Logical) Indicates whether ln(y+1) should be applied to the response data of the dose response curves. Default: FALSE.

(Numeric) Defines the number of bootstrap samples for EC50 estimation. Use nboot.dr = 0 to disable bootstrapping. Default: 0.

Data that passed to the function as gcTable.

Dataframe containing condition identifiers, fit options, and results of the dose-response analysis.

List of all drBootSpline objects generated by the call of growth.drBootSpline for each distinct experiment.

List of all drFitSpline objects generated by the call of growth.drFitSpline for each distinct experiment.

Object of class grofit.control containing list of options passed to the function as control.

Vector of concentration values.

Vector of response parameter values of the same length as conc.

(Character) The name of the analyzed condition

A grofit.control object created with growth.control, defining relevant fitting options.

Vector of concentration values.

Vector of response parameter values of the same length as conc.

(Character) The name of the analyzed condition

A grofit.control object created with growth.control, defining relevant fitting options.

Raw data provided to the function as conc.

Raw data for the response parameter provided to the function as test.

(Character) Identifies the tested condition

Fitted concentration values.

Fitted response values.

smooth.spline object generated by the smooth.spline function.

x and y values of lowess spline fit on raw data. Used to call smooth.spline.

List of parameters estimated from dose response curve fit.

(Logical) Indicates whether a spline could fitted successfully to data.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

Object of class grofit.control containing list of options passed to the function as control.

Vector of the independent variable (usually: time).

Vector of dependent variable (usually: growth values).

(Character) The name of the analyzed sample.

A grofit.control object created with growth.control, defining relevant fitting options.

Raw time values provided to the function as time.

Raw growth data provided to the function as data.

(Character) Identifies the tested sample.

Table of time values per column, resulting from each spline fit of the bootstrap.

Table of growth values per column, resulting from each spline fit of the bootstrap.

List of gcFitSpline object, created by growth.gcFitSpline for each resample of the bootstrap.

Vector of estimated lambda (lag time) values from each bootstrap entry.

Vector of estimated mu (maximum growth rate) values from each bootstrap entry.

Vector of estimated A (maximum growth) values from each bootstrap entry.

Vector of estimated integral values from each bootstrap entry.

(Logical) Indicates the success of the bootstrapping operation.

Object of class grofit.control containing list of options passed to the function as control.

(optional) A matrix containing time values for each sample.

Either...

1. a grodata object created with read_data or parse_data,

2. a list containing a 'time' matrix as well as 'growth' and, if appropriate, a 'fluorescence' dataframes, or

3. a dataframe containing growth values (if a time matrix is provided as separate argument).

A grofit.control object created with growth.control, defining relevant fitting options.

Run linear fits and bootstrapping operations in parallel using all but one available processor cores

Further arguments passed to the shiny app.

Raw time matrix passed to the function as time.

Raw growth dataframe passed to the function as data.

Table with growth parameters and related statistics for each growth curve evaluation performed by the function. This table, which is also returned by the generic summary.gcFit method applied to a gcFit object, is used as an input for growth.drFit.

List of all gcFitLinear objects, generated by the call of growth.gcFitLinear. Note: access to each object in the list via double brace: gcFittedLinear[[#n]].

List of all gcFitModel objects, generated by the call of growth.gcFitModel. Note: access to each object in the list via double brace: gcFittedModels[[#n]].

List of all gcFitSpline objects, generated by the call of growth.gcFitSpline. Note: access to each object via double brace: gcFittedSplines[[#n]].

List of all gcBootSpline objects, generated by the call of growth.gcBootSpline. Note: access to each object via double brace: gcFittedSplines[[#n]].

Object of class grofit.control containing list of options passed to the function as control.

Vector of the independent variable (usually: time).

Vector of dependent variable (usually: growth values).

(Character) The name of the analyzed sample.

(Numeric, between 0 an 1) Define what fraction of mu_{max} the slope of regression windows adjacent to the window with highest slope should have to be included in the overall linear fit.

A grofit.control object created with growth.control, defining relevant fitting options.

(Logical) Indicates whether ln(x+1) should be applied to the time data for linear and spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for linear fits. Default: TRUE

(Numeric) Indicate whether only growth values above a certain threshold should be considered for linear regressions.

(Numeric) Indicate whether only growth values below a certain threshold should be considered for linear regressions.

(Numeric) Minimum time value considered for linear and spline fits.

(Numeric) Minimum time value considered for linear and spline fits.

(Numeric) Manually define the size of the sliding window . If NULL, h is calculated for each samples based on the number of measurements in the growth phase of the plot.

(Numeric) R² threshold for growth.gcFitLinear

(Numeric) Relative standard deviation (RSD) threshold for calculated slope in growth.gcFitLinear

(Numeric) Enter the minimum percentage of growth increase that a linear regression should cover.

(Logical) Shall growth.gcFitLinear try to extract growth parameters for two different growth phases (as observed with, e.g., diauxic shifts) (TRUE) or not (FALSE)?

Raw time values provided to the function as time.

Raw growth data provided to the function as data.

Filtered time values used for the heuristic linear method.

Filtered growth values.

Log-transformed, filtered growth values used for the heuristic linear method.

(Character) Identifies the tested sample.

Linear function used for plotting the tangent at mumax.

lm object; result of the final call of lm to perform the linear regression.

List of determined growth parameters:

Index of data points used for the linear regression.

Index of data points used for the linear regression for the second growth phase.

Object of class grofit.control containing list of options passed to the function as control.

of the linear regression.

of the linear regression for the second growth phase.

(Logical) Indicates whether linear regression was successfully performed on the data.

(Logical) Indicates whether a second growth phase was identified.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

Vector of the independent variable (usually time).

Vector of dependent variable (usually growth values).

(Character) The name of the analyzed sample.

A grofit.control object created with growth.control, defining relevant fitting options.

Raw time values provided to the function as time.

Raw growth data provided to the function as data.

(Character) Identifies the tested sample.

Fitted time values.

Fitted growth values.

List of determined growth parameters.

(Character) The model that obtained the fit with the lowest AIC, determined by AIC.

nls object for the chosen model generated by the nls function.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

(Logical) Indicates whether a parametric model was successfully fitted on the data.

Object of class grofit.control containing list of options passed to the function as control.

Vector of the independent variable (usually time).

Vector of dependent variable (usually: growth values).

(Character) The name of the analyzed sample.

A grofit.control object created with growth.control, defining relevant fitting options.

(Logical) Shall growth.gcFitSpline try to extract growth parameters for two different growth phases (as observed with, e.g., diauxic shifts) (TRUE) or not (FALSE)?

Raw time values provided to the function as time.

Raw growth data provided to the function as data.

Filtered time values used for the spline fit.

Filtered growth values used for the spline fit.

(Character) Identifies the tested sample.

Fitted time values.

Fitted growth values.

List of determined growth parameters.

smooth.spline object generated by the smooth.spline function.

list of time ('x') and growth ('y') values describing the first derivative of the spline fit.

(Logical) Indicates whether the performed fit is reliable (to be set manually).

(Logical) Indicates whether a spline fit was successfully performed on the data.

(Logical) Indicates whether a second growth phase was identified.

Object of class grofit.control containing list of options passed to the function as control.

A grofit object created with growth.workflow.

(Character) The path or name of the folder in which the report files are created. If NULL, the folder will be named with a combination of 'Report.growth_' and the current date and time.

Character or NULL Define the name of the report files. If NULL, the files will be named with a combination of 'GrowthReport_' and the current date and time.

(Logical) Display results of dose-response analysis (TRUE) or not (FALSE).

(Character) Define the file format for the report, PDF ('pdf') and/or HTML ('html'). Default: (c('pdf', 'html'))

(Logical) Shall all plots generated in the report be exported as individual PDF and PNG files TRUE or not FALSE?

(Logical) Create plots using all but one available processor cores (TRUE) or only a single core (FALSE).

Further arguments passed to create a report. Currently supported:

• mean.grp: Define groups to combine into common plots in the report based on sample identifiers. Partial matches with sample/group names are accepted. Can be 'all', a string vector, or a list of string vectors. Note: The maximum number of sample groups (with unique condition/concentration indicators) is 50. If you have more than 50 groups, option 'all' will produce the error ! Insufficient values in manual scale. [Number] needed but only 50 provided.

• mean.conc: Define concentrations to combine into common plots in the report. Can be a numeric vector, or a list of numeric vectors.

A grodata object created with read_data or parse_data, or a list containing a 'time' matrix as well as a 'growth' dataframe.

(optional) A matrix containing time values for each sample.

(optional) A dataframe containing growth data (if a time matrix is provided as separate argument).

(Logical) Perform dose-response analysis (TRUE) or not (FALSE).

('all', a string vector, or a list of string vectors) Define groups to combine into common plots in the final report based on sample identifiers (if report == TRUE). Partial matches with sample/group names are accepted. Note: The maximum number of sample groups (with unique condition/concentration indicators) is 50. If you have more than 50 groups, option 'all' will produce the error ! Insufficient values in manual scale. [Number] needed but only 50 provided.

(A numeric vector, or a list of numeric vectors) Define concentrations to combine into common plots in the final report (if report == TRUE).

(Logical) Indicates whether the program should stop when negative growth values or NA values appear (TRUE). Otherwise, the program removes these values silently (FALSE). Improper values may be caused by incorrect data or input errors. Default: FALSE.

(Logical) Determines if negative values which occur during bootstrap should be removed (TRUE) or kept (FALSE). Note: Infinite values are always removed. Default: TRUE.

(Logical) Indicates whether grofit messages (information about current growth curve, EC50 values etc.) should be displayed (FALSE) or not (TRUE). This option is meant to speed up the high-throughput processing data. Note: warnings are still displayed. Default: FALSE.

(Character or character vector) Indicates whether the program should perform a linear regression ('l'), model fit ('m'), spline fit ('s'), or all ('a'). Combinations can be freely chosen by providing a character vector, e.g. fit.opt = c('l', 's') Default: fit.opt = c('l', 's').

(Numeric) Minimum time value considered for linear and spline fits.

(Numeric) Maximum time value considered for linear and spline fits.

(Numeric) Indicate whether only growth values above a certain threshold should be considered for linear regressions or spline fits.

(Numeric) Indicate whether only growth values below a certain threshold should be considered for linear regressions or spline fits.

(Logical) Indicates whether ln(x+1) should be applied to the time data for linear and spline fits. Default: FALSE.

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for linear fits. Default: TRUE

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for spline fits. Default: TRUE

(Logical) Indicates whether ln(y/y0) should be applied to the growth data for model fits. Default: TRUE

(Logical) Shall growth.gcFitLinear and growth.gcFitSpline try to extract growth parameters for two different growth phases (as observed with, e.g., diauxic shifts) (TRUE) or not (FALSE)?

(Numeric) Manually define the size of the sliding window used in growth.gcFitLinear If NULL, h is calculated for each samples based on the number of measurements in the growth phase of the plot.

(Numeric) R² threshold for growth.gcFitLinear

(Numeric) Relative standard deviation (RSD) threshold for calculated slope in growth.gcFitLinear

(Numeric) Threshold for the minimum fraction of growth increase a linear regression window should cover. Default: 0.05 (5%).

(Logical) Controls whether the fit of each growth curve and method is controlled manually by the user. If TRUE, each fit is visualized in the Plots pane and the user can adjust fitting parameters and confirm the reliability of each fit per sample. Default: TRUE.

(Numeric) Number of bootstrap samples used for nonparametric growth curve fitting with growth.gcBootSpline. Use nboot.gc = 0 to disable the bootstrap. Default: 0

(Numeric) Parameter describing the smoothness of the spline fit; usually (not necessary) within (0;1]. smooth.gc=NULL causes the program to query an optimal value via cross validation techniques. Especially for datasets with few data points the option NULL might cause a too small smoothing parameter. This can result a too tight fit that is susceptible to measurement errors (thus overestimating growth rates) or produce an error in smooth.spline or lead to an overestimation. The usage of a fixed value is recommended for reproducible results across samples. See ?smooth.spline for further details. Default: 0.55

(Character) Vector providing the names of the parametric models which should be fitted to the data. Default: c('logistic', 'richards', 'gompertz', 'gompertz.exp', 'huang', 'baranyi').

(Character) Define the method used to perform a dose-responde analysis: smooth spline fit ('spline') or model fitting ('model').

(Character) Provide a list of models from the R package 'drc' to include in the dose-response analysis (if dr.method = 'model'). If more than one model is provided, the best-fitting model will be chosen based on the Akaike Information Criterion.

(Numeric) Define a threshold for growth. Only if any growth value in a sample is greater than growth.thresh (default: 1.5) times the start growth, further computations are performed. Else, a message is returned.

(Numeric) Minimum number of different values for the response parameter one should have for estimating a dose response curve. Note: All fit procedures require at least six unique values. Default: 6.

(Character or numeric) The response parameter in the output table to be used for creating a dose response curve. See growth.drFit for further details. Default: 'mu.linfit', which represents the maximum slope of the linear regression. Typical options include: 'mu.linfit', 'lambda.linfit', 'dY.linfit', 'mu.spline', 'dY.spline', 'mu.model', and 'A.model'.

(Numeric) Smoothing parameter used in the spline fit by smooth.spline during dose response curve estimation. Usually (not necessesary) in (0; 1]. See documentation of smooth.spline for further details. Default: NULL.

(Logical) Indicates whether ln(x+1) should be applied to the concentration data of the dose response curves. Default: FALSE.

(Logical) Indicates whether ln(y+1) should be applied to the response data of the dose response curves. Default: FALSE.

(Numeric) Defines the number of bootstrap samples for EC50 estimation. Use nboot.dr = 0 to disable bootstrapping. Default: 0.

(Character or NULL) Create a PDF ('pdf') and/or HTML ('html') report after running all computations. Define NULL if no report should be created. Default: (c('pdf', 'html'))

Character or NULL Define the name of a folder in which all result files are stored. If NULL, the folder will be named with a combination of 'GrowthResults_' and the current date and time.

Character or NULL Define the name of the report files. If NULL, the files will be named with a combination of 'GrowthReport_' and the current date and time.

(Logical) Export all figures created in the report as separate PNG and PDF files (TRUE) or not (FALSE). Only effective if report != NULL.

(Logical) Create tab-separated TXT files containing calculated growth parameters and dose-response analysis results as well as an .RData file for the resulting grofit object.

Run linear fits and bootstrapping operations in parallel using all but one available processor cores

Further arguments passed to the shiny app.

Raw time matrix passed to the function as time (if no grofit object is provided).

Raw growth dataframe passed to the function as data (if no grofit object is provided).

gcFit object created with the call of growth.gcFit.

drFit object created with the call of growth.drFit.

Experimental design table inherited from grodata or created from the identifier columns (columns 1-3) in data.

Object of class grofit.control created with the call of growth.control.

vector of values with minima and maxima

Threshold to consider minima or maxima

linear model (lm) object

vector of independent variable (e.g. time).

vector of dependent variable (concentration of organisms).

index of first value used for a window.

with of the window (number of data).

Numeric vector of x values.

Numeric vector of y values with the same length as x.

A dataframe created by reading a table file with read_file

(Character) A table file with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' containing raw plate reader (or similar device) data.

(Character) A table file in column format with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' with 'well', 'ID', 'replicate', and 'concentration' in the first row. Used to assign sample information to wells in a plate.

(Character) The name of the software/device used to export the plate reader data.

(NULL or string) Convert time values with a formula provided in the form 'y = function(x)'. For example: convert.time = 'y = 24 * x'

(Numeric or Character) Number or name of the sheets in XLS or XLSX files containing experimental data or mapping information, respectively (optional).

(Character) separator used in CSV data files (ignored for other file types). Default: ";"

(Character) decimal separator used in CSV, TSV or TXT files with measurements and mapping information, respectively.

(Logical) Shall blank values be subtracted from values within the same experiment (TRUE, the default) or not (FALSE).

(Character or NULL) Provide an equation in the form 'y = function(x)' (for example: 'y = x^2 * 0.3 - 0.5') to convert growth and fluorescence values. This can be used to, e.g., convert plate reader absorbance values into OD₆₀₀ or fluorescence intensity into molecule concentrations. Caution!: When utilizing calibration, carefully consider whether or not blanks were subtracted to determine the calibration before selecting the input subtract.blank = TRUE.

(Character string) Normalize fluorescence values by either diving by 'growth' or by fluorescence2 values ('fl2').

A dataframe created by reading a table file with read_file

A dataframe created by reading a table file with read_file

A drBootSpline object created with growth.drBootSpline or stored within a grofit or drFit object created with growth.workflow or growth.drFit, respectively.

(Numeric) Shape of the raw data symbols.

(Numeric or Character) Color used to plot the raw data.

(Numeric or Character) Color used to plot the splines.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric) Spline line width.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Logical) Indicate whether both dose-response curves and parameter plots shall be shown within the same window.

Further arguments to refine the generated base R plot.

object of class drFit, created with growth.drFit.

(Logical) Combine the dose-response analysis results of all conditions into a single plot (TRUE) or not (FALSE).

(String or vector of strings) Define conditions to combine into a single plot (if combine = TRUE). Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(String or vector of strings) Define conditions to exclude from the plot (if combine = TRUE). Partial matches with sample/group names are accepted.

(Numeric) Shape of the raw data symbols.

(Numeric) Size of the raw data points.

(Numeric) Base font size.

(Numeric or character) Define colors for different conditions.

(Numeric) Line width of the individual splines.

(Logical) Show pointed horizontal and vertical lines at the EC50 values (TRUE) or not (FALSE).

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis.

(Character) Optional: Provide a title for the x-axis.

(Logical) Log-transform the y-axis of the plot (TRUE) or not (FALSE)?

(Logical) Log-transform the x-axis of the plot (TRUE) or not (FALSE)?

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

Object of class drFitFLModel, created with fl.drFitModel.

(Logical) Show pointed horizontal and vertical lines at the EC50 value (TRUE) or not (FALSE).

(Logical) If TRUE the x axis is broken provided this axis is logarithmic (using functionality in the CRAN package 'plotrix').

(Numeric) Specifying the break point below which the dose is zero (the amount of stretching on the dose axis above zero in order to create the visual illusion of a logarithmic scale including 0). The default is the base-10 value corresponding to the rounded value of the minimum of the log10 values of all positive dose values. This argument is only working for logarithmic dose axes.

(Numeric) Number of breaks on the x-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

(Numeric) Number of breaks on the y-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.#' @param pch (Numeric) Size of the raw data circles.

(Character) String which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "x". The empty string "" yields the original axes.

(Numeric) Symbol used to plot data points.

(Numeric or Character) Color used to plot the splines.

(Numeric or Character) Color used to plot the raw data.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis as a vector in the form c(l, u).

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u).

(Numeric) Line width.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated base R plot.

object of class drFitModel, created with growth.drFitModel.

(Character) Specify how to plot the data. There are currently 5 options: "average" (averages and fitted curve(s); default), "none" (only the fitted curve(s)), "obs" (only the data points), "all" (all data points and fitted curve(s)), "bars" (averages and fitted curve(s) with model-based standard errors (see Details)), and "confidence" (confidence bands for fitted curve(s)).

(Logical) Show pointed horizontal and vertical lines at the EC50 values (TRUE) or not (FALSE).

(Logical) If TRUE then add to already existing plot.

(Logical) If TRUE the x axis is broken provided this axis is logarithmic (using functionality in the CRAN package 'plotrix').

(Numeric) Specifying the break point below which the dose is zero (the amount of stretching on the dose axis above zero in order to create the visual illusion of a logarithmic scale including 0). The default is the base-10 value corresponding to the rounded value of the minimum of the log10 values of all positive dose values. This argument is only working for logarithmic dose axes.

(Numeric) Number of points in the grid used for plotting the fitted curves.

(Character) String which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "x". The empty string "" yields the original axes.

(Numeric) Number of breaks on the x-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

(Numeric) Number of breaks on the y-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric) Symbol used to plot data points.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis annotations.

(Numeric) Font size of axis titles.

(Logical or a vector of colors) If TRUE default colours are used. If FALSE (default) no colors are used.

(Numeric) Line width.

(Numeric) Specify the line type.

(Character) An optional label for the x axis.

(Character) An optional label for the y axis.

(Logical) If TRUE a legend is displayed.

(Character) Specify the legend text (the position of the upper right corner of the legend box).

(Numeric) Vector of length 2 giving the position of the legend.

numeric specifying the legend text size.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

object of class drFitSpline, created with growth.drFitSpline.

(Logical) Shall the fitted spline be added to an existing plot? TRUE is used internally by plot.drBootSpline.

(Logical) Show pointed horizontal and vertical lines at the EC50 value (TRUE) or not (FALSE).

("x", "y", or "xy") Display the x- or y-axis on a logarithmic scale.

(Numeric) Shape of the raw data symbols.

(Numeric or character) Spline line colour.

(Numeric or character) Contour color of the raw data circles.

(Numeric) Size of the raw data symbols.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis.

(Character) Optional: Provide a title for the x-axis.

(Numeric) Line width of spline.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated base R plot.

object of class drFit, created with growth.drFit.

(Logical) Show pointed horizontal and vertical lines at the EC50 values (TRUE) or not (FALSE).

(Character) String which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "x". The empty string "" yields the original axes.

(Numeric) Shape of the raw data symbols.

(Logical) If TRUE the x axis is broken provided this axis is logarithmic (using functionality in the CRAN package 'plotrix').

(Numeric) Specifying the break point below which the dose is zero (the amount of stretching on the dose axis above zero in order to create the visual illusion of a logarithmic scale including 0). The default is the base-10 value corresponding to the rounded value of the minimum of the log10 values of all positive dose values. This argument is only working for logarithmic dose axes.

(Numeric) Number of breaks on the x-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

(Numeric) Number of breaks on the y-axis (if not log-transformed). The breaks are generated using pretty. Thus, the final number of breaks can deviate from the user input.

(Numeric or character) Spline line colour.

(Numeric or character) Contour color of the raw data circles.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric) Line width of the individual splines.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

A grofit, drFit, drTable, or flFitRes object obtained with growth.workflow, growth.drFit, fl.drFit, or fl.workflow.

(Character) The parameter used to compare different sample groups. Any name of a column containing numeric values in gcTable (which is stored within grofit or gcFit objects) can be used as input. Useful options are: 'y.max', 'y.min', 'fc', 'K', or 'n' for fluorescence dose-response analyses with dr.type = 'model' in the control argument, or 'EC50', 'yEC50', 'drboot.meanEC50', 'drboot.meanEC50y'.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric) Base font size.

(Character) Name of the reference condition, to which parameter values are normalized. Partially matching strings are tolerated as long as they can uniquely identify the condition.

(Numeric) Font size for sample labels below x-axis.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

A flFit, flFitRes, or grodata object created with flFit, fl.workflow or read_data

(Character) Indicate, which type of fluorescence data should be displayed.

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(Logical) Display the mean and standard deviation of groups with replicates (TRUE) or plot each sample individually (FALSE)?

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Logical) Log-transform the y-axis of the growth plot (TRUE) or not (FALSE)?

(Logical) Log-transform the y-axis of the fluorescence plot (TRUE) or not (FALSE)?

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(vector of strings) Define a color palette used to draw the plots. If NULL, default palettes are chosen based on the number of groups/samples within the plot. Note: The number of provided colors should at least match the number of groups/samples.

(Logical) Shall samples within the same group but with different concentrations be shown in different shades of the same color?

(String vector) Define the colors used to display sample groups with identical concentrations. The number of selected color palettes must be at least the number of displayed groups. The order of the chosen palettes corresponds to the oder of conditions in the legend. Available options: "Green", "Oranges", "Purple", "Cyan", "Grey", "Red", "Blue", and "Magenta".

(Numeric) Base font size.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the growth plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the fluorescence plot as a vector in the form c(l, u).

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the x-axis of both fluorescence and growth plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Character) Optional: Provide a title for the y-axis of the growth plot.

(Character) Optional: Provide a title for the y-axis of the fluorescence plot.

(Numeric) Line width of the individual plots.

(Character) Position of the legend. One of "bottom", "top", "left", "right".

(Numeric) Number of columns in the legend.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

Object of class flBootSpline, created with flBootSpline.

(Numeric) Size of the raw data circles.

(Numeric or Character) Color used to plot the raw data.

(Logical) Show the derivatives (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).

(Numeric or Character) Color used to plot the splines.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric) Spline line width.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the fluorescence curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both fluorescence curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Logical) Indicate whether both growth curves and parameter plots shall be shown within the same window.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

A flFittedLinear object created with flFitLinear or stored within a flFitRes or flFit object created with fl.workflow or flFit, respectively.

("x" or "y") Display the x- or y-axis on a logarithmic scale.

("fit" or "diagnostics") Display either the results of the linear fit on the raw data or statistical evaluation of the linear regression.

(Numeric) Shape of the raw data symbols.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric) Line width.

(Character string) Enter color either by name (e.g., red, blue, coral3) or via their hexadecimal code (e.g., #AE4371, #CCFF00FF, #0066FFFF). A full list of colors available by name can be found at http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis as a vector in the form c(l, u).

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u).

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated base R plot.

A flFitRes, flFit, or grodata object created with fl.workflow containing fluorescence data.

(Character) Indicate, which type of fluorescence data should be displayed.

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(Logical) Display the mean and standard deviation of groups with replicates (TRUE) or plot each sample individually (FALSE)?

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Logical) Log-transform the y-axis of the plot (TRUE) or not (FALSE)?

(Logical) Show derivatives over time in a separate panel below the plot (TRUE) or not (FALSE)?

(Numeric) Number of breaks on the y-axis. The breaks are generated using axisTicks(). Thus, the final number of breaks can deviate from the user input.

(vector of strings) Define a color palette used to draw the plots. If NULL, default palettes are chosen based on the number of groups/samples within the plot. Note: The number of provided colors should at least match the number of groups/samples.

(Logical) Shall samples within the same group but with different concentrations be shown in different shades of the same color?

(String vector) Define the colors used to display sample groups with identical concentrations. The number of selected color palettes must be at least the number of displayed groups. The order of the chosen palettes corresponds to the oder of conditions in the legend. Available options: "Green", "Oranges", "Purple", "Cyan", "Grey", "Red", "Blue", and "Magenta".

(Numeric) Base font size.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the fluorescence curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the x-axis of both fluorescence curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the fluorescence curve plot.

(Character) Optional: Provide a title for the x-axis of both fluorescence curve and derivative plots.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the derivative plot.

(Numeric) Line width of the individual plots.

(Character) Position of the legend. One of "bottom", "top", "left", "right".

(Numeric) Number of columns in the legend.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

Object of class flFitSpline, created with flFitSpline.

(Logical) Shall the fitted spline be added to an existing plot? TRUE is used internally by plot.flBootSpline.

(Logical) Display raw growth as circles (TRUE) or not (FALSE).

(Logical) Show the slope at the maximum slope (TRUE) or not (FALSE).

(Logical) Show the derivative (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).

(Logical) Only for add = TRUE: add the current spline to the existing plot (FALSE).

(Logical) Log-transform the y-axis (TRUE) or not (FALSE).

(Numeric) Base font size.

(Numeric) Symbol used to plot data points.

(Numeric or character) Contour color of the raw data circles.

(Numeric or character) Spline line colour.

(Numeric) Size of the raw data points.

(Numeric) Spline line width.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the fluorescence curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both fluorescence curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric) Number of breaks on the y-axis. The breaks are generated using axisTicks(). Thus, the final number of breaks can deviate from the user input.

(Character) Optional: Provide a title for the y-axis of the growth curve plot.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Character) Optional: Provide a title for the y-axis of the derivative plot.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Width of the exported image in inches.

(Numeric) Height of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

object of class gcBootSpline, created with growth.gcBootSpline.

(Numeric) Symbol used to plot data points.

(Numeric or character) Contour color of the raw data circles.

(Logical) Show the derivatives (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).

(Numeric or character) Spline line colour.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric) Spline line width.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Logical) Indicate whether both growth curves and parameter plots shall be shown within the same window.

Further arguments to refine the generated base R plot.

A gcFittedLinear object created with growth.gcFitLinear or stored within a grofit or gcFit object created with growth.workflow or growth.gcFit, respectively.

("x" or "y") Display the x- or y-axis on a logarithmic scale.

("fit" or "diagnostics") Display either the results of the linear fit on the raw data or statistical evaluation of the linear regression.

(Numeric) Shape of the raw data symbols.

(Numeric) Size of the raw data points.

(Numeric) Font size of axis titles.

(Numeric) Font size of axis annotations.

(Numeric) Line width.

(Character string) Enter color either by name (e.g., red, blue, coral3) or via their hexadecimal code (e.g., #AE4371, #CCFF00FF, #0066FFFF). A full list of colors available by name can be found at http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis as a vector in the form c(l, u).

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u).

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE).

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated base R plot.

A gcFittedModel object created with growth.gcFitModel or stored within a grofit or gcFit object created with growth.workflow or growth.gcFit, respectively.

(Logical) Show the raw data within the plot (TRUE) or not (FALSE).

(Numeric) Symbol used to plot data points.

(Numeric or Character) Color used to plot the raw data.

(Logical) Show the equation of the fitted model within the plot (TRUE) or not (FALSE).

(Numeric) Provide a value to scale the size of the displayed equation.

(Numeric or Character) Color used to plot the fitted model.

(Numeric) Base font size.

(Numeric) Size of the raw data points.

(Numeric) Spline line width.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated ggplot2 plot.

object of class gcFitSpline, created with growth.gcFitSpline.

(Logical) Shall the fitted spline be added to an existing plot? TRUE is used internally by plot.gcBootSpline.

(Logical) Display raw growth as circles (TRUE) or not (FALSE).

(Logical) Show the slope at the maximum growth rate (TRUE) or not (FALSE).

(Logical) Show the derivative (i.e., slope) over time in a secondary plot (TRUE) or not (FALSE).

(Logical) Only for add = TRUE: add the current spline to the existing plot (FALSE).

(Logical) Log-transform the y-axis (TRUE) or not (FALSE).

(Numeric) Symbol used to plot data points.

(Numeric or character) Contour color of the raw data circles.

(Numeric or character) Spline line colour.

(Numeric) Base font size.

(Numeric) Size of the raw data points.

(Numeric) Spline line width.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(Character) Optional: Provide a title for the y-axis of the growth curve plot.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Character) Optional: Provide a title for the y-axis of the derivative plot.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Width of the exported image in inches.

(Numeric) Height of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

Further arguments to refine the generated base R plot (if add = TRUE.

A grofit or flFitRes object created with growth.workflow or fl.workflow containing spline fits.

(Character) Plot either raw data (data.type = "raw") or the spline fit results

(Character) The parameter used to compare different sample groups. Any name of a column containing numeric values in gcTable (which is stored within grofit or gcFit objects) can be used as input. Useful options are: 'mu.linfit', 'lambda.linfit', 'dY.linfit', 'A.linfit', 'mu.model', 'lambda.model', 'A.model', 'mu.spline', 'lambda.spline', 'A.spline', 'dY.spline', 'integral.spline', 'mu.bt', 'lambda.bt', 'A.bt', 'integral.bt'

(Character string) Choose one of 'Green', 'Orange', 'Purple', 'Magenta', 'Grey', 'Blue', 'Grey', 'Red', 'Cyan', 'Brown', or 'Mint' to visualize the value of the parameter chosen as param for each sample or condition.

(Logical) Shall the colors in the chosen pal be inverted (TRUE) or not FALSE?

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign. The order of strings within the vector defines the order of samples within the grid.

(Logical) Shall samples/conditions be ordered as entered in IDs (TRUE) or alphabetically (FALSE)?

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Logical) Display the mean and standard deviation of groups with replicates (TRUE) or plot each sample individually (FALSE)?

(Logical) Log-transform the y-axis of the plot (TRUE) or not (FALSE)?#'

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(Logical) Shall the samples/conditions be sorted with concentrations in rows and groups in columns?

(Numeric) Defines the number of rows in the grid if sort_by_conc is FALSE.

(Numeric) Base font size.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the color scale applied to param as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the growth curve plot.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Numeric) Line width of the individual plots.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

A grodata object created with read_data or parse_data.

(Character) Plot either raw growth (data.type = "growth"), raw fluorescence (data.type = "fl"), or fluorescence normalized to growth (data.type = "norm.fl").

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(Logical) Display the mean and standard deviation of groups with replicates (TRUE) or plot each sample individually (FALSE)?

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Logical) Log-transform the y-axis of the plot (TRUE) or not (FALSE)?

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(vector of strings) Define a color palette used to draw the plots. If NULL, default palettes are chosen based on the number of groups/samples within the plot. Note: The number of provided colors should at least match the number of groups/samples.

(Logical) Shall samples within the same group but with different concentrations be shown in different shades of the same color?

(String vector) Define the colors used to display sample groups with identical concentrations. The number of selected color palettes must be at least the number of displayed groups. The order of the chosen palettes corresponds to the oder of conditions in the legend. Available options: "Green", "Oranges", "Purple", "Cyan", "Grey", "Red", "Blue", and "Magenta".

(Numeric) Base font size.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the growth curve plot.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Numeric) Line width of the individual plots.

(Character) Position of the legend. One of "bottom", "top", "left", "right".

(Numeric) Number of columns in the legend.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

A grofit object created with growth.workflow containing spline fits.

(optional) Additional grofit objects created in separate workflows for joint plotting in a single graph.

(Character) Plot either raw data (data.type = "raw") or the spline fit results

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Logical) Display the mean and standard deviation of groups with replicates (TRUE) or plot each sample individually (FALSE)?

(Logical) Log-transform the y-axis of the plot (TRUE) or not (FALSE)?

(Logical) Show derivatives over time in a separate panel below the plot (TRUE) or not (FALSE)?

(Numeric) Number of breaks on the y-axis. The breaks are generated using scales::pretty_breaks. Thus, the final number of breaks can deviate from the user input.

(vector of strings) Define a color palette used to draw the plots. If NULL, default palettes are chosen based on the number of groups/samples within the plot. Note: The number of provided colors should at least match the number of groups/samples.

(Logical) Shall samples within the same group but with different concentrations be shown in different shades of the same color?

(String vector) Define the colors used to display sample groups with identical concentrations. The number of selected color palettes must be at least the number of displayed groups. The order of the chosen palettes corresponds to the oder of conditions in the legend. Available options: "Green", "Oranges", "Purple", "Cyan", "Grey", "Red", "Blue", and "Magenta".

(Numeric) Base font size.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the y-axis of the growth curve plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds of the x-axis of both growth curve and derivative plots as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the growth curve plot.

(Character) Optional: Provide a title for the x-axis of both growth curve and derivative plots.

(Numeric vector with two elements) Optional: Provide the lower (l) and upper (u) bounds on the y-axis of the derivative plot as a vector in the form c(l, u). If only the lower or upper bound should be fixed, provide c(l, NA) or c(NA, u), respectively.

(Character) Optional: Provide a title for the y-axis of the derivative plot.

(Numeric) Line width of the individual plots.

(Character) Position of the legend. One of "bottom", "top", "left", "right".

(Numeric) Number of columns in the legend.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

A grofit, gcFit, or gcTable object obtained with growth.workflow or growth.gcFit.

(Character) The parameter used to compare different sample groups. Any name of a column containing numeric values in gcTable (which is stored within grofit or gcFit objects) can be used as input. Useful options are: 'mu.linfit', 'lambda.linfit', 'dY.linfit', 'A.linfit', 'mu.model', 'lambda.model', 'A.model', 'mu.spline', 'lambda.spline', 'A.spline', 'dY.spline', 'integral.spline', 'mu.bt', 'lambda.bt', 'A.bt', 'integral.bt'

(String or vector of strings) Define samples or groups (if mean = TRUE) to combine into a single plot based on exact matches with entries in the label or condition columns of grofit$expdesign.

(String or vector of strings) Define groups to combine into a single plot. Partial matches with sample/group names are accepted. If NULL, all samples are considered. Note: Ensure to use unique substrings to extract groups of interest. If the name of one condition is included in its entirety within the name of other conditions, it cannot be extracted individually.

(Numeric or numeric vector) Define concentrations to combine into a single plot. If NULL, all concentrations are considered. Note: Ensure to use unique concentration values to extract groups of interest. If the concentration value of one condition is included in its entirety within the name of other conditions (e.g., the dataset contains '1', '10', and '100', code = 10 will select both '10 and '100'), it cannot be extracted individually.

(String or vector of strings) Define groups to exclude from the plot. Partial matches with sample/group names are accepted.

(Numeric or numeric vector) Define concentrations to exclude from the plot.

(Character) Name of the reference condition, to which parameter values are normalized. Partially matching strings are tolerated as long as they can uniquely identify the condition.

(Numeric) Concentration of the reference condition, to which parameter values are normalized.

(Logical) Shall the columns be sorted in order of ascending concentrations (TRUE) or by sample groups FALSE?

(vector of strings) Define a color palette used to draw the columns. If NULL, default palettes are chosen. Note: The number of provided colors should at least match the number of groups.

(Numeric) Base font size.

(Numeric) Font size for sample labels below x-axis.

(Numeric) The size of the symbols indicating replicate values. Default: 2.5

(Character) Position of the legend. One of "bottom", "top", "left", "right".

(Numeric) Number of columns in the legend.

(Logical) Show the generated plot in the Plots pane (TRUE) or not (FALSE). If FALSE, a ggplot object is returned.

(Logical) Export the generated plot as PDF and PNG files (TRUE) or not (FALSE).

(Numeric) Height of the exported image in inches.

(Numeric) Width of the exported image in inches.

(Character) Name or path to a folder in which the exported files are stored. If NULL, a "Plots" folder is created in the current working directory to store the files in.

(Character) The name of the PDF and PNG files if export = TRUE. If NULL, a name will be automatically generated including the chosen parameter.

Additional arguments. This has currently no effect and is only meant to fulfill the requirements of a generic function.

Numeric value, number of data sets. If d is a vector, only the first entry is used.

Numeric value, start growth. If t is a vector, only the first entry is used.

Numeric value, number of time points per data set. If t is a vector, only the first entry is used.

Numeric value, maximum slope. If mu is a vector, only the first entry is used.

Numeric value, lag-phase. If lambda is a vector, only the first entry is used.

Numeric value, maximum growth. If A is a vector, only the first entry is used.

Character string, condition label If label is a vector, only the first entry is used.

numeric matrix of size dxt, each row represent the time points for which growth data is simulated and stored in each row of data.

data.frame of size dx(3+t), 1. column, character as an experiment identifier; 2. column: Replicate number; 3. column: concentration of substrate of a compound under which the experiment is obtained; 4.-(3+t). column: growth data corresponding to the time points in time.