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Generic plot function for drFitSpline objects.

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

codeplot.drFitSpline generates the spline fit plot for response-parameter vs. concentration data

Usage

# S3 method for drFitSpline
plot(
  x,
  add = FALSE,
  ec50line = TRUE,
  log = "",
  pch = 16,
  colSpline = 1,
  colData = 1,
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  y.lim = NULL,
  x.lim = NULL,
  y.title = NULL,
  x.title = NULL,
  lwd = 2,
  plot = TRUE,
  export = FALSE,
  height = 7,
  width = 9,
  out.dir = NULL,
  ...
)

Arguments

x

object of class drFitSpline, created with growth.drFitSpline.

add

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

ec50line

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

log

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

pch

(Numeric) Shape of the raw data symbols.

colSpline

(Numeric or character) Spline line colour.

colData

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

cex.point

(Numeric) Size of the raw data symbols.

cex.lab

(Numeric) Font size of axis titles.

cex.axis

(Numeric) Font size of axis annotations.

y.lim

(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.

x.lim

(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.

y.title

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

x.title

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

lwd

(Numeric) Line width of spline.

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.

...

Further arguments to refine the generated base R plot.

Value

A plot with the nonparametric dose-response fit.

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.drFitSpline(conc, response, drID = "test",
                     control = growth.control(log.x.dr = TRUE, smooth.dr = 0.8))
#> 
#> 
#> === Dose response curve estimation ================
#> --- EC 50 -----------------------------------------
#> --> test
#> xEC50 1.62740039535265 yEC50 0.472023372440819
#> --> Original scale 
#> xEC50 4.09062389301508 yEC50 0.472023372440819
#> 
#> 

print(summary(TestRun))
#>     EC50     yEC50 EC50.orig yEC50.orig test
#> 1 1.6274 0.4720234  4.090624  0.4720234   NA
plot(TestRun)