plot.flFitLinear {QurvE}

Generic plot function for flcFittedLinear objects. Plot the results of a linear regression on ln-transformed data

Description

plot.flFitLinear shows the results of a linear regression and visualizes raw data, data points included in the fit, the tangent obtained by linear regression, and the lag time.

Usage

## S3 method for class 'flFitLinear'
plot(
  x,
  log = "",
  which = c("fit", "diagnostics", "fit_diagnostics"),
  pch = 21,
  cex.point = 1,
  cex.lab = 1.5,
  cex.axis = 1.3,
  lwd = 2,
  color = "firebrick3",
  y.lim = NULL,
  x.lim = NULL,
  plot = TRUE,
  export = FALSE,
  height = ifelse(which == "fit", 7, 5),
  width = ifelse(which == "fit", 9, 9),
  out.dir = NULL,
  ...
)

Arguments

x

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

log

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

which

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

pch

(Numeric) Shape of the raw data symbols.

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) Line width.

color

(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

y.lim

(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).

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).

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 linear fit.

Examples

# load example dataset
input <- read_data(data.growth = system.file("lac_promoters_growth.txt", package = "QurvE"),
                   data.fl = system.file("lac_promoters_fluorescence.txt", package = "QurvE"),
                   csvsep = "\t",
                   csvsep.fl = "\t")

# Extract time and normalized fluorescence data for single sample
time <- input$time[4,]
data <- input$norm.fluorescence[4,-(1:3)] # Remove identifier columns

# Perform linear fit
TestFit <- flFitLinear(time = time,
                       fl_data = data,
                       ID = "TestFit",
                       control = fl.control(fit.opt = "l", x_type = "time",
                       lin.R2 = 0.95, lin.RSD = 0.1,
                       lin.h = 20))

plot(TestFit)