doseResponse: Dose-Response Plots with Error Bars

Description Usage Arguments

View source: R/platereader.R

Description

plots a continuous value for each well as a function of an amount of a substance and generates error bars for all replicates at a given amount; returns the plotted mean values and error bar ranges.

Usage

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doseResponse(map, wells, val, amount = "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 amount and some calculated value in column val, eg. results from grofit or growthrates

wells

a list of well IDs to be used in the plot

val

the name of a column in map containing numeric values that should be plotted on y-axis

amount

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 amount, 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 amount should have the same color, only the first color for a given amount is used; such colors are automatically assigned from a color ramp mapped to the numerical range of amount 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 "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 val; 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 val

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 Nov. 9, 2018, 5:38 p.m.