oneParamPlot: Used to plot a single parameter

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

Used to plot a single parameter

Description

This function creates a pdf figure of plots showing the results of the imageJ analysis for resistance (radius from the disk, RAD), sensitivity (slope) and tolerance (fraction of growth above RAD, FoG).

Usage

oneParamPlot(
  projectName,
  type,
  param = "RAD20",
  ymin = 0,
  ymax = 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")
param	what parameter to plot (supported: "RAD20", "RAD50", "RAD80", "FoG20", "FoG50", "FoG80", "slope"), default = "RAD20"
ymin	a numeric value indicating the minimum y value plotted in each plot
ymax	a numeric value indicating the maximum y value plotted in each plot
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 values as a barplot (barplot = TRUE) or dotplot (barplot = FALSE), default = TRUE. Only possible when type = "ag"

Details

Basic parameter plotting functions to plot a single parameter. Input can be the dataframe from either createDataframe type="df" or from aggregateData type=="ag".

Value

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

See Also

twoParamPlot for a similar figure with two parameters or threeParamPlot for a similar figure with three parameters

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