doseResponse.box: Dose-Response Box-Plots

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

Description

Plots a continuous value for each well as a function of an dose of a substance and make boxplots for all replicates at a given dose. Note that this is deprecated, and plots with error bars can be generated instead by function doseResponse.

Usage

doseResponse.box(
  map,
  wells,
  response,
  dose = "amount",
  substance = "substance",
  color = "color",
  na.y = 0,
  ylim,
  xnum = FALSE,
  xlab,
  ylab
)

Arguments

map	a plate layout map with columns dose and some calculated value in column response, eg. results from grofit or growthrates
wells	a list of well IDs to be used in the plot
response	the name of a column in map containing numeric values that should be plotted on y-axis
dose	the name of a column in map providing numeric values that should be plotted on x-axis, typically a substance added to wells in multiple replicates; the default value "amount" is automatically generated from appropriate plate layout files by link{readPlateMap}
substance	the name of a column in map providing the names of the substance in dose, used as x-axis label; if it doesn't correspond to a column, its value is directly used as label
color	the name of a column in map providing colors for each well; NOTE, that wells with the same dose should have the same color, only the first color for a given dose is used; Colors are automatically assigned from a color ramp mapped to the numerical range of dose by link{readPlateMap}
na.y	value to be used to plot replicates with NA in column response; set to NA to supress plotting
ylim	limits of the y-axis
xnum	use numerical x-axis instead of default categorical
xlab	alternative label for the x-axis, default is to use argument substance, or if this is a column in map, the substance indicated there
ylab	alternative label for the y-axis, default is to use argument response

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.