plotMixlowData {mixlow}R Documentation

Plot prepared data

Description

Plots results obtained from the prepareData function.

Usage

plotMixlowData(mixlowData, trays=getTrays(mixlowData), ask, 
    showBlanks= TRUE)

Arguments

mixlowData A list obtained from the prepareData function.
trays A vector of strings indicating the trays for which data should be plotted.
ask Logical. If TRUE (and the R session is interactive) the user is asked for input, before a new figure is drawn.
showBlanks Logical. If TRUE, data from the optical control wells (“blanks”) in a tray are included in the graph. Default is TRUE

Details

This function is used to plot prepared data. Adjusted concentration-response data are plotted, and mean responses over replicate wells receiving identical drug concentrations are connected by a line. The adjustments subtracted from the raw data (see PrepareData function) can be included in the plot by setting showBlanks equal to TRUE. For purposes of plotting on a log-scale plot, drug concentrations of zero are changed to 1/1000 of the lowest nonzero drug concentration. This adjustment only affects plotting, not analysis.

Value

A list of length equal to the number of trays with components:

drug Drug name
cell Cell line name
Units Units of measurement
title Title for plot
adjResp Adjusted response data
adjConc Adjusted concentration data
ylim y limits of plot
meanLineY Response values for mean line between group replicates
meanLineX Concentration values for mean line between group replicates
blankY Responses from optical control wells
blankX Concentrations for optical control wells
blankLineY Responses for optical control data line
blankLineX Concentrations for optical control data line

Author(s)

John Boik jcboik@stanford.edu

See Also

readDataFile, prepareData

Examples

# mixlowData data object is obtained using the prepareData function
data(mixlowData)
trays <- getTrays(mixlowData)
saved_mixlow_graphing_data <- plotMixlowData(mixlowData=mixlowData, 
    trays= trays[1:9], ask=FALSE, showBlanks= TRUE)

[Package mixlow version 0.01.1 Index]