timeLinePlot: Plot channel values against time

In flowViz: Visualization for flow cytometry

Description

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

Usage

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

## S4 method for signature 'flowSet,character'
timeLinePlot(x, channel,
  type = c("stacked", "scaled", "native", "frequency"), col = NULL,
  ylab = sampleNames(x), binSize, varCut = 1, ...)

## S4 method for signature 'flowFrame,character'
timeLinePlot(x, channel, ...)

## S4 method for signature 'ANY,missing'
timeLinePlot(x, channel, ...)

Arguments

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.

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.

Author(s)

F. Hahne

See Also

flowFrame, flowSet

Examples

library(flowCore)
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)

flowViz documentation built on Nov. 8, 2020, 7:53 p.m.