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Generic plot function for gcBootSpline objects.

Source: R/growth_plots.R
plot.drBootSpline.Rd

Generic plot function for gcBootSpline objects.

Usage

# S3 method for drBootSpline
plot(
  x,
  pch = 19,
  colData = 1,
  colSpline = "black",
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  lwd = 2,
  plot = TRUE,
  export = FALSE,
  height = 7,
  width = 9,
  out.dir = NULL,
  combine = FALSE,
  ...
)

Arguments

x

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

pch

(Numeric) Shape of the raw data symbols.

colData

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

colSpline

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

cex.point

(Numeric) Size of the raw data points.

cex.lab

(Numeric) Font size of axis titles.

cex.axis

(Numeric) Font size of axis annotations.

lwd

(Numeric) Spline line width.

plot

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

export

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

height

(Numeric) Height of the exported image in inches.

width

(Numeric) Width of the exported image in inches.

out.dir

(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.

combine

(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.

Value

A plot with the all dose-response spline fits from the bootstrapping operation.

Examples

conc <- c(0, rev(unlist(lapply(1:18, function(x) 10*(2/3)^x))),10)
response <- c(1/(1+exp(-0.7*(4-conc[-20])))+stats::rnorm(19)/50, 0)

TestRun <- growth.drBootSpline(conc, response, drID = "test",
        control = growth.control(log.x.dr = TRUE, smooth.dr = 0.8, nboot.dr = 50))
#> === Bootstrapping of dose response curve ==========
#> --- EC 50 -----------------------------------------
#> 
#> Mean  :  0.899544564649059 StDev :  0.0702732286376704 
#> 90% CI:  0.89723257542688 90% CI:  0.901856553871239
#> 95% CI:  0.896789854086463 95% CI:  0.902299275211656
#> 
#> 
#> --- EC 50 in original scale -----------------------
#> 
#> Mean  :  1.45848317599923 
#> 90% CI:  1.45280575499046 90% CI:  1.46417373832963
#> 95% CI:  1.451720085881 95% CI:  1.46526492215745
#> 

print(summary(TestRun))
#>   drboot.meanEC50 drboot.sdEC50 drboot.meanEC50y drboot.sdEC50y
#> 1       0.8995446    0.07027323         0.541395     0.09390099
#>   drboot.ci90EC50.lo drboot.ci90EC50.up drboot.ci95EC50.lo drboot.ci95EC50.up
#> 1          0.7839451           1.015144           0.761809            1.03728
#>   drboot.meanEC50.orig drboot.ci90EC50.orig.lo drboot.ci90EC50.orig.up
#> 1             1.458483                1.190095                1.759761
#>   drboot.ci95EC50.orig.lo drboot.ci95EC50.orig.up
#> 1                1.142148                1.821532
plot(TestRun, combine = TRUE)