plotData: Plot the data.

Description Usage Arguments Details See Also Examples

View source: R/plotData.R

Description

plotData allows to visualize the data and, possibly, the selected samples and peaks.

Usage

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plotData(data, channels, startTime = NA, endTime = NA, ymin = NA,
  ymax = NA, peaks = NA, samples = NA, ytext = (-0.005),
  savePlot = FALSE)

Arguments

data

input data (formatted as data.frame with 4 columns: green, orange, blue, time)

channels

a vector with the name of the channels we want to plot (e.g. channels=c("green", "blue") to plot the green and the blue channel)

startTime

initial time point to be plot. Default is NA, plots from the first time point in the data

ymin, ymax

lower and upper limit of the y axes. Default is NA, for automatically defined range to include all data.

peaks

peaks computed using the function peaksSelection

samples

samples selected using the function samplesSelection

ytext

position in the y axes of the sample names/numbers if samples argument is specified

savePlot

if FALSE, the plot is not saved; if TRUE plot is saved with default file name; if string, plot is saved with given filename. Plot is saved in .png format

Details

This function is used to visualize the desired range of data showing values for one or more channels. It can be used also to plot the peaks selected on one channel using the function peaksSelection and/or the samples identified using samplesSelection.

See Also

peaksSelection to select peaks in a specific channel, samplesSelection to separate data in samples

Examples

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data(BxPC3_data, package="BraDiPluS")
plotData(data=MyData, channels=c("blue", "green", "orange"))

res <- samplesSelection(data=MyData, BCchannel="blue",BCthr=0.01, BCminLength=100, distThr=16, plotMyData=F, barcodePos="before")
samples<-res$samples
plotData(data=MyData, channels=c("blue", "orange", "green"), samples = samples)

BCpeaks <- peaksSelection(MyData, channel="blue")
plotData(data=MyData, channels=c("blue", "orange", "green"), peaks = BCpeaks)

saezlab/BraDiPluS documentation built on May 20, 2018, 4:42 a.m.