twoParamPlot: Used to plot the RAD and FoG results

In acgerstein/diskImageR: A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

Used to plot the RAD and FoG results

Description

This function creates a pdf figure of plots showing the results of the imageJ analysis for resistance (RAD) and tolerance (FoG).

Usage

twoParamPlot(
  projectName,
  type,
  RAD = "RAD20",
  FoG = "FoG20",
  RADmin = 30,
  tolMax = 100,
  width = 6,
  height = 4,
  xlabels = "line",
  xlabAngle = NA,
  order = NA,
  orderFactor = "line",
  overwrite = TRUE,
  savePDF = TRUE,
  popUp = TRUE,
  barplot = TRUE
)

Arguments

projectName	the short name to be used for the project
type	specify whether the dataset to use is a dataframe with all data ("df") or an aggregated dataframe ("ag")
RAD	specify the RAD (radius) parameter to be plotted ("RAD20", "RAD50" or "RAD80"), default = "RAD20".
FoG	specify the FoG (fraction of growth) parameter to be plotted ("FoG20", "FoG50" or "FoG80"), default = "FoG20".
RADmin	minimum distance from the disk for resistance plot (minimum y axis value), default = 30.
tolMax	maximum y axis value for tolerance plot. Note tolerance is coverted to a percent, default = 100.
width	a numeric value indicating the width of the pdf file generated
height	a numeric value indicating the height of the pdf file generated
xlabels	either a vector containing the desired x-axis labels, or a single value indicating the column name that contains the values to use (likely either the 'line' column or one of the type columns), default = "line".
xlabAngle	indicates whether to print the x axis labels on a angle, if a number is provided this will be the angle used. The defauilt is not to plot on an angle, default = NA.
order	can be either "factor" or "custom". If custom, supply a numberial vector the same length as the dataframe to indicate the desired order. If factor, supply the column name in ordeFactor to be used to factor.
orderFactor	if order = "factor" supply the column name to be used to factor.
overwrite	a logical value indicating whether to overwrite existing figures created on the same day for the same project name
savePDF	a logical value indicating whether to save a PDF file or open a new quartz window. Defaults to TRUE (saves a pdf file).
popUp	a logical value indicating whether to pop up the figure after it has been created
barplot	whether to plot tolerance as a barplot (barplot = TRUE) or dotplot (barplot = FALSE), default = TRUE. Only possible when type = "ag"

Details

Basic parameter plotting functions to plot RAD and FoG parameter plots. Input can be the dataframe from either createDataframe type="df" or from aggregateData type=="ag". The default is to plot RAD as a dotplot and tolerance as a barplot, though tolerance can also be plotted as a dotplot with barplot=FALSE (currently there is not support to plot RAD as a barplot in this framework).

Value

Either a pdf figure figure (projectName_RAD-FoG.pdf) saved to the 'figures' directory or a figure on screen

See Also

oneParamPlot for a similar figure with one parameter or threeParamPlot for a similar figure with three parameters

acgerstein/diskImageR documentation built on May 18, 2024, 4:15 a.m.