plot.HT_fit: Plot a dose response curve from a HTfit object

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

Description

If the curve cannot be fit (meaning that the optimization method used by the drm() method from the drc package failes to converge) then the summarized points will be plotted without a curve connecting them.

Usage

## S3 method for class 'HT_fit'
plot(x, ..., bar_multiple = 2, summary_method = "mean",
  show_EC50 = FALSE, show_legend = FALSE, show_x_log_tics = TRUE,
  show_x_exponent = TRUE, log_axis_x = TRUE)

Arguments

x	HTfit object
...	standard parameters for plot function
bar_multiple	multiplier for standard error bars, default 2
summary_method	summary method for points to plot in timecourse, one of ("mean", "median"), defaults "mean"
show_EC50	show dotted vertical lines at EC50 values if they are fit, default FALSE
show_legend	show a legend, default FALSE
show_x_log_tics	if axes==TRUE and this parameter is TRUE, draw tics between each power of 10 scaled appropriately. If axes==TRUE and this parameter is FALSE, omit ticks between powers of 10. Default TRUE.
show_x_exponent	If axes==TRUE and this parameter is TRUE, show labels on X axis as 10^2, 10^3, ... . If axes==TRUE and this parameter is FALSE, show labels on X axis as an exponent (2, 3, ... ). Default TRUE.
log_axis_x	logical. If TRUE, X axis is to be logarithmic; if FALSE, X axis is original scale. Default is TRUE.

Value

none

See Also

fit_DRC

Examples

sample_types = rep( c(rep("line1",3), rep("line2",3)), 5)
treatments = c(rep("DMSO",6), rep("drug",24))
concentrations = c( rep(0,6),rep(200,6), rep(500,6),rep(1000,6),rep(5000,6))
values=c(100,99,100,90,91,92,99,97,99,89,87,88,86,89,88,56,59,58,66,65,67,
         25,23,24,42,43,46,4,5,9)
hours = rep(48, length(values))
plate_id = "plate_1"
ds = create_dataset( sample_types=sample_types, treatments=treatments, 
                     concentrations=concentrations, hours=hours, 
                     values=values, plate_id=plate_id, 
                     negative_control = "DMSO")
library(drc)
# Fit model using three-parameter log-logistic function
fit_1=fit_DRC(ds, sample_types=c("line1", "line2"), treatments=c("drug"), 
        hour = 48, fct=drc::LL.3() )
plot(fit_1)
plot(fit_1, show_EC50=FALSE, show_legend=FALSE, lwd=3,col=c("black", "gold"),
     xlim=c(0, 1e4), xlab="concentration nM", 
     ylab="surviving fraction")
legend(1.5, 0.3, c("Line 1", "Line 2"), col=c("black", "gold"), pch=15)

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