Compare Two or More Sets of Already-Unmixed Data

Lays out biplots for two or more pre-unmixed data sets (matrices or data frames of the same panel) as a grid, one row per data set, so that the same channel pairs can be compared side-by-side across conditions (for example, cells vs. beads, or before vs. after a correction step).

Channels are paired up sequentially rather than plotted N x N: for channels = c("APC", "FITC", "PE", "PerCP", "BV421") the pairs are APC x FITC, PE x PerCP, and BV421 x APC (the first channel is repeated to complete the last pair when an odd number of channels is requested). Each row uses create.biplot() for every pair, and the panels are stitched together with cowplot::plot_grid().

If gate.boundary is supplied and the scatter.param columns are present in every data set, apply.gate() is used to gate every data set to that boundary before plotting. If any data set is missing a scatter column, the gate is not applied to any of them (a warning names which data set(s) were missing it), so that every row in the comparison reflects the same population.

If data.list is a named list, the names are used as row labels on the right of the grid. If unnamed, and data.list was constructed inline as list(...) at the call site, the deparsed expression for each element (i.e. the variable name passed in) is used instead.

Usage

compare.unmixed.data(
  data.list,
  channels,
  asp,
  gate.boundary = NULL,
  scatter.param = asp$default.scatter.parameter,
  variants = NULL,
  spread.kappa = 2,
  x.min = -5000,
  x.max = asp$expr.data.max,
  y.min = -5000,
  y.max = asp$expr.data.max,
  x.width.basis = -1000,
  y.width.basis = -1000,
  max.points = 5e+05,
  color.palette = "rainbow",
  panel.width = 3,
  row.height = 3,
  label.width = 1,
  label.size = 12,
  label.angle = -90,
  save = TRUE,
  title = "unmix_comparison",
  output.dir = NULL
)

Arguments

data.list: A list of two or more matrices or data frames of unmixed flow cytometry data, one per data set to compare. Every element must have named columns. Column names do not need to match exactly across data sets – see channels below.
channels: Character vector of channel names to plot, in the order they should be paired (see Description). Must resolve to at least 2 channels present in every element of data.list after the intersect described below.
asp: The AutoSpectral parameter list, prepared using get.autospectral.param(). Passed through to create.biplot() for every panel, and supplies the default for scatter.param.
gate.boundary: Optional gate boundary, as returned by define.gate.landmarks(), define.gate.density(), or do.gate() – a list containing at least numeric x and y components describing the polygon vertices. When supplied, every data set is gated with apply.gate() before plotting, provided all data sets carry scatter.param. Default NULL (no gating).
scatter.param: Character vector of length 2 giving the names of the two scatter columns to gate on, passed to apply.gate(). Only used when gate.boundary is supplied. Default asp$default.scatter.parameter.
variants: The variant list returned by get.spectral.variants(), passed through to every create.biplot() call for reference curves. Default NULL (no reference curves).
spread.kappa: Numeric, passed through to create.biplot(). Default 2.
x.min, y.min: Numeric, axis minima (data units) passed through to create.biplot(). Default -5000 for both.
x.max, y.max: Numeric, axis maxima (data units) passed through to create.biplot(). Default asp$expr.data.max for both.
x.width.basis, y.width.basis: Numeric, biexponential width bases passed through to create.biplot(). Default -1000 for both.
max.points: Numeric, per-panel point cap passed through to create.biplot(). Default 5e5.
color.palette: Character, passed through to create.biplot(). Default "rainbow".
panel.width, row.height: Numeric, width and height (inches) of a single biplot panel, used to size the saved figure. Defaults 3 and 3.
label.width: Numeric, width (inches) reserved for the row-label column on the right of the figure. Default 1.
label.size: Numeric, font size (points) for the row labels. Default 12.
label.angle: Numeric, rotation angle (degrees) for the row labels. Default -90 (reads bottom-to-top, matching a facet_grid right strip).
save: Logical, if TRUE (default), saves a JPEG file to output.dir. Otherwise the combined plot is only printed.
title: Character, used as the JPEG filename stem. Default "unmix_comparison".
output.dir: Optional output directory. Default NULL, in which case the current working directory is used.

Value

Invisibly, the combined cowplot object.

Usage

Arguments

Value

See also