plot_fit_statistic: Plot a dose response curve summary values across one or more...

In DavidQuigley/HTDoseResponseCurve: Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

Description

Used to generate a line and dot plot of one or more AUC or EC50 values across a series of time points. All of the values in the fit_stats data frame will be plotted. Observations that do not meet the criteria specified in the alpha parameter are plotted using open values (e.g. pch=1). Observations where the minimum EC50 exceeds the obs_min parameter can be plotted using a user-specified value for the pch parameter; by default this is pch=13.

Usage

plot_fit_statistic(fit_stats, statistic, ..., alpha = 1, obs_min = NA)

Arguments

fit_stats	data frame returned by call to fit_statistics
statistic	statistic to plot, must be one of AUC, EC50
...	standard parameters for plot function
alpha	cut-off to distinguish results with an ANOVA_P_value that is considered statistically significant, plotted as closed circles. Defaults to 1.
obs_min	cut-off to distinguish results where the minimum observed response across any dose is no greater than obs_min. Useful for restricting plots to those values that acheived a result such as a Surviving Fraction below 50 percent. Defaults to NA, which plots everything.

Value

data frames with plotted points, colors. Useful for drawing a legend.

Examples

pkg = "HTDoseResponseCurve"
fn_map = system.file("extdata","sample_data_384_platemap.txt",package=pkg)
fn_data = system.file("extdata", "sample_data_384.xlsx", package = pkg)
plate_map = read_platemap_from_Incucyte_XML( fn_map )
plate_data = read_plates_from_Incucyte_export( fn_data, "p1", 
                                               number_of_wells=384)
plate_data$hours = round(plate_data$hours)
ds = combine_data_and_map( plate_data, plate_map, negative_control = "DMSO" )
ds = ds[ds$treatment=="drug13",]
fits = fit_statistics(ds, fct = drc::LL.3() )
res=plot_fit_statistic( fits, "AUC", ylim=c(0, 6) ) 

DavidQuigley/HTDoseResponseCurve documentation built on Jan. 23, 2021, 5:10 a.m.