qfa.plot: Plots fitted model and data for all the colonies in results...

In qfa: Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces

Description

Produces a multipage pdf of growth curves. Each page corresponds to a single plate and growth curves are arrayed on the page according to their position on the plate. Both observations (red crosses) and the fitted growth curve from qfa.fit (solid black curves) are shown for each culture. The time at which the maximum slope of the observed growth curve on the log scale occurs (solid blue line) and the time at which the maximum slope of the raw observed data occurs (dashed blue line) are also indicated. Where available, various fitness estimates are displayed for each culture, together with culture genotype. These .pdfs are useful for visually checking quality of model fit & data.

Usage

qfa.plot(file,results,d,fmt="%Y-%m-%d_%H-%M-%S",barcodes=c(),
master.plates=c(),treatments=c(),screen.names=c(),screenIDs=c(),
maxg=0,maxt=0,logify=FALSE,densityCol="Growth",curves=TRUE,
ylabel="Cell density (AU)",ptype="p",ming=1e-5)

Arguments

file	The file to output the plots to.
results	The output of qfa.fit which contains the fitted curve parameters of colony growth you wish to plot.
d	The original data.frame fed to qfa.fit containing all of the timecourse data
fmt	The format in which Date.Time of measurement and inoculation time are stored
barcodes	Plot only for the plates with barcodes in this character vector; all by default.
master.plates	Plot only for the plates from master.plates in this character vector; all by default.
treatments	Plot only for the plates with treatments in this character vector; all by default.
screen.names	Plot only for the plates with screen.names in this character vector; all by default.
screenIDs	Plot only for the plates with screenIDs in this character vector; all by default.
maxg	Upper cell density (y-axis limit) for all growth curve plots. Default value is zero. If maxg=0, then upper fitnesses are chosen automatically to show all datapoints.
maxt	Growth curve is plotted from time t = 0 to maxt.
logify	Boolean indicating whether growth curve plots should be on a semilog scale. Cell density (y-axis) only.
densityCol	Name of column in data frame d which contains cell density estimate. Note that the image analysis software Colonyzer provides several possible alternatives.
curves	Boolean indicating whether fitted model curves should be drawn. Useful to set this to false when generating diagnostic, data-only growth curves. To do this, set curves = FALSE and pass the same (data) object twice, as both the d and results arguments. For example: qfa.plot("test.pdf",df,df,curves=FALSE)
ylabel	String for y-axis label on growth curve plots.
ptype	Plot type for data: "p": points, "l": lines, "b": both
ming	Minimum growth value (y-axis) for plotting.

qfa documentation built on Feb. 22, 2020, 3:01 a.m.