doseResponse: Dose-Response Plots with Error Bars

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 generates error bars for all replicates at a given dose; returns the plotted mean values and error bar ranges.

Usage

doseResponse(
  map,
  wells,
  response,
  dose = "amount",
  substance = "substance",
  col = "black",
  pch = 1,
  bartype = "range",
  barl = 0.05,
  all = FALSE,
  line = TRUE,
  na.y = 0,
  add = FALSE,
  ylim,
  xlim,
  ylab,
  xlab,
  verb = TRUE,
  ...
)

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
col	either a valid color representation or the name of a column in map providing colors for each well or a, if wells is a named list of wells, a named vector of colors with matching names. NOTE for the second case, that wells with the same dose should have the same color, only the first color for a given dose is used; such colors are automatically assigned from a color ramp mapped to the numerical range of dose by readPlateMap, see amountColors;
pch	pch of the mean value points
bartype	type of the error bars, "range" for the full range of the data, where the average value will be the median; or "ci95" for the 95% confidence interval, "sd" for the standard deviation, or "se" for the standard error where the average value will be the mean; TODO: implement boxplot-like quantiles
barl	length of the horizontal lines of error bars (argument length of function arrows)
all	logical indicating whether to plot all data points additionally to error bars
line	logical indicating whether to plot a line connecting the mean values
na.y	value to be used to plot replicates with NA in column response; set to NA to supress plotting
add	add data to existing plot
ylim	limits of the y-axis
xlim	limits of the x-axis
ylab	alternative label for the y-axis, default is to use argument response
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
verb	print progress messages
...	arguments passed on to the main setup plot

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