timeLinePlot-methods {flowViz} | R Documentation |
Plots values of one parameter for each flowFrame in a flowSet against time.
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.
A numeric vector of quality scores.
General usage:
timeLinePlot(x, channel, type=c("stacked", "scaled",
"native"), col, ylab=names(x), binSize, varCut=1, ...)
flowFrame
or
flowSet
containing the data to be plotted.\[my - signma *
varCut, my + sigma * varCut\]
will contribute to a positive
quality score value.
flowFrame
we only plot a single parameter
against time. flowSet
, we plot the lines for a single parameter
against time for each flowFrame
in the set.
F. Hahne
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)