qfa.AggregateCurves: Plot all data measurement points including model curves...

In JulBaer/baQFA: Quantitative Fitness Analysis Version 2

Plot all data measurement points including model curves grouped by userinput in a ggplot object

Description

This functions creates a ggplot object with the input data.frames from either Read.Colonyzer or GC2QFA functions (data.frame GC) and the model fits from a subsequent call to qfa.fit2 (data.frame results) of the same data.frame. The data can also be displayed without the model-fits. For this, the user inputs the same data.frame for results and GC which was generated by either Read.Colonyzer or GC2QFA. The qfa.AggregateCurves functions lets the user specify by which factors the plot should be facetted and colored. These factors need to be present in both results and GC data.frame as a column.

Usage

qfa.AggregateCurves(
  results,
  GC,
  plotCol = "ORF",
  plotFacet = "ScreenID",
  yname = "Growth",
  legName = NA,
  PlotName = NA,
  markb = F,
  TimeFormat = NA
)

Arguments

results	data.frame. Usually, the output data.frame of qfa.fit2 to create model curves. It can also be the output data.frame of Read.Colonyzer or GC2QFA if the data without model curves should be displayed
GC	data.frame. The data.frame used as an input for qfa.fit2 to generate the results data.frame. If the results data.frame is the output of either Read.Colonyzer or GC2QFA, then GC needs to be the same data.frame
plotCol	String. The name of the column header which should be used for coloring of the curves
plotFacet	String. The name of the column header which should be used for facetting of the plots
yname	String. Label of the y-axis
legName	String. Label for the color legend
PlotName	String. Title for the plot
markb	logical. Indicator if the b parameter of the Gompertz model should be marked as a colored vertical line. Ignored if another model was used to create the results data.frame
TimeFormat	String. Either "d" for days or "h" for hours. If set to NA and results contains model-fits, the TimeFormat specified in the call to qfa.fit2 is used

Value

This function just 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="All", filename="Example_Gmp_fitness.pdf")
# Create aggregated curves plot
a = qfa.AggregateCurves(GmpFit, qfa.testdata, plotFacet="ORF", yname="Intesity [AU]", legName="Strain", markb=F)
# Demonstrating subsequent ggplot object manipulations:
a = a + ggplot2::ggtitle("Alternate title")
a

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