qfaFitnessPlot: Boxplots displying specified fitness measurements, colored...

In JulBaer/baQFA: Quantitative Fitness Analysis Version 2

Boxplots displying specified fitness measurements, colored and facetted by user-input

Description

This function creates ggplot boxplots visualizing fitness measurements. It is integrated into the makeFitness2 function as well. There are three methods used to define fitness: 1) By multiplying maximal doubling potential (MDP) and maximal doubling rate (MDR) accoring to the original QFA work. 2) By divinding the maximal absolute growth rate (r) of the Gompertz model with the time to reach r (b). 3) By dividing the model-free estimation of r with the model free estimation of b. The user can specify which should be plotted by setting the plotFitness parameters to either "All", "MDR" (1) "Gmp" (2) or "ModelFree" (3). Factor used on the x-axis is defined with plotX. Additionally, coloring and facetting factor names can be specified with plotFill and plotFacet. If filename is specified, the plots will be saved as a pdf with the specified name.

Usage

qfaFitnessPlot(
  results,
  plotFitness = "no",
  filename = NA,
  plotX = "ORF",
  plotFacet = "ScreenID",
  plotFill = "Treatment"
)

Arguments

results	This is the output data.frame of the qfa.fit2 function
plotFitness	String. Either set to "All" to plot all three types of fitness measurements if the Gompertz model was used, otherwise only MDR-based and modelfree fitness estimates are plotted. If set to "MDR" only MDR*MDP based fitness estimates are displayed. If set to "Gmp" only Gompertz model based fitness estimates are displayed. If set to "ModelFree" only model free fitness estimates are displayed.
filename	If this is anything else than NA, a pdf file will be saved into the current working directory named filename
plotX	String. Name of the column of the results data.frame used as a factor seperating boxplots on the x-axis
plotFill	String. Name of the column of the results data.frame used as a factor coloring the boxplots
plotoFacet	String. Name of the column of the results data.frame used as a factor creaeting facets

Value

This function plots the ggplot object if not used with an assignment. If it is called as an assignment, the return is a ggplot object which can further be modified by the user if desired.

Examples

#qfa.testdata was generated with the call in the Not run section
#(these files are not included in the package)
data(qfa.testdata)
#Strip non-experimental edge cultures
qfa.testdata = qfa.testdata[(qfa.testdata$Row!=1) & (qfa.testdata$Col!=1) & (qfa.testdata$Row!=8) & (qfa.testdata$Col!=12),]
# Define which measure of cell density to use
qfa.testdata$Growth = qfa.testdata$Intensity
GmpFit = qfa.fit2(qfa.testdata, inocguess=NULL, detectThresh=0, globalOpt=F, AUCLim=NA, TimeFormat="h", Model="Gmp")
# Construct fitness measures
GmpFit = makeFitness2(GmpFit, AUCLim=NA, plotFitness="no")
qfaFitnessPlot(GmpFit, plotFitness="All", filename="Example_Gmp_fitness.pdf")

JulBaer/baQFA documentation built on Feb. 19, 2023, 10:32 p.m.