timeLinePlot-methods {flowViz} | R Documentation

## Plot channel values against time

### Description

Plots values of one parameter for each flowFrame in a flowSet against time.

### Details

Plotting flow cytometry data against the time domain can help to identify problems with the fluidics or drifts in the instrument setting during measurement runs.

This function creates plots for all flowFrames in a flowSet for a given parameter against time. A barplot legend indicates the deviation from the median for each sample. There is also a flowFrame method, which will create a plot for a single flowFrame only.

In addition, the function computes a quality score for each frame, which essentially is the sum of the positive distances of each bin mean from a frame-specific confidence interval, divided by the number of bins. Values larger than zero indicate a problem.

### Value

A numeric vector of quality scores.

### Methods

General usage:

`timeLinePlot(x, channel, type=c("stacked", "scaled", "native"), col, ylab=names(x), binSize, varCut=1, ...)`

x
  An object of class `flowFrame` or `flowSet` containing the data to be plotted.
channel
  The parameter for which the data is to be plotted
type
  One in 'stacked', 'scaled' or 'native'. 'stacked' will plot the measurements for the frames on top of each other. 'scaled' will align the median values around zero and 'native' will plot the values in the original dimensions of the measurement range.
col
  Optional color parameter.
ylab
  The axis annotation to add on the y-axis for stacked plots.
binSize
  The number of events per bin. If not set, a reasonable default is computed.
varCut
  The cutoff in the adjusted variance to which the quality score is computed. Basically, all values that are outside of the confidence interval defined by `\[my - signma * varCut, my + sigma * varCut\]` will contribute to a positive quality score value.
...
  Further arguments that are passed on to the base plotting functions.

x = "ANY", channel = "missing"
  This casts a useful error message about missing inputs.
x = "flowFrame", channel = "character"
  For a `flowFrame` we only plot a single parameter against time.
x = "flowSet", channel = "character"
  For a `flowSet`, we plot the lines for a single parameter against time for each `flowFrame` in the set.

### Author(s)

F. Hahne

### See Also

`flowFrame`, `flowSet`

### Examples

    data(GvHD)
    opar <- par(ask=TRUE)

    res <- timeLinePlot(GvHD[[1]], "SSC-H")
    res

    res <- timeLinePlot(GvHD, "SSC-H")

    res <- timeLinePlot(GvHD, "SSC-H", type="scaled", varCut=4)

    res <- timeLinePlot(GvHD[1:4], "SSC-H", type="native", binSize=50)

    par(opar)

[Package flowViz version 1.8.0 Index]