m \(\times\) n Unmixed Biplot Grid

Produces a grid of scatter biplots comparing a set of m target fluorophores (x-axis) against every other channel in the dataset (y-axis), and saves the result as a multi-panel PDF. Each target fluorophore defines one row of panels; the columns correspond to all other selected channels.

Data are downsampled once to max.points events before any panel is drawn, so all panels share the same cell population. Axis minima are auto-scaled per channel using the 1st percentile of the data, floored at the user-supplied x.min / y.min.

Panels can use either geom_hex (default, fastest) or the standard geom_scattermore + stat_density_2d combination from create.biplot().

Usage

unmixed.mxn.plot(
  unmixed.data,
  fluorophore,
  asp,
  channels = NULL,
  max.points = 50000,
  title = "mxn_biplot",
  biplot.size = 3,
  n.col = NULL,
  x.min = -1000,
  y.min = -1000,
  x.width.basis = -1000,
  y.width.basis = -1000,
  use.hex = TRUE,
  hex.bins = 64,
  color.palette = "viridis",
  output.dir = "."
)

Arguments

unmixed.data

Either a character string giving the path to an unmixed FCS file, or a numeric matrix / data.frame whose columns are fluorophore channels and whose rows are cells.

fluorophore

Character vector of length \(m\). Names of the target fluorophores to place on the x-axis (one row of panels per entry). Every element must be present in colnames(unmixed.data) (or the FCS columns).

asp

The AutoSpectral parameter list, created by get.autospectral.param().

channels

Optional character vector. Subset of channels to use as y-axis columns. When NULL (default) all columns except those in fluorophore are used. Must be present in the data if supplied.

max.points

Integer. Total number of events to retain after a single random downsample applied before drawing any panel. Default 5e4.

title

Character string used as the PDF filename stem and as the overall plot title. Default "mxn_biplot".

biplot.size

Numeric. Edge length in inches of each individual panel. Default 3.

n.col

Integer. Number of panel columns per page. When NULL (default) this is set to the number of y-axis channels, giving one row of panels per target fluorophore on a single page.

x.min

Numeric. Floor for the auto-scaled x-axis minimum (data units). The actual minimum used is min(auto, x.min). Default -1000.

y.min

Numeric. Floor for the auto-scaled y-axis minimum (data units). Default -1000.

x.width.basis

Numeric. Width basis for the biexponential x-axis transform (passed to flowWorkspace::flowjo_biexp()). Default -1000.

y.width.basis

Numeric. Width basis for the biexponential y-axis transform. Default -1000.

use.hex

Logical. When TRUE (default), panels are rendered with ggplot2::geom_hex() for speed. When FALSE, reverts to scattermore::geom_scattermore() + ggplot2::stat_density_2d().

hex.bins

Integer. Number of bins for geom_hex in each dimension. Ignored when use.hex = FALSE. Default 64.

color.palette

Character string. Viridis palette name ("viridis", "magma", "inferno", "plasma", "cividis", "rocket", "mako", "turbo") or "rainbow" to use the package default gradient. Default "viridis".

output.dir

Character string. Directory for the output PDF. Created automatically if absent. Default ".".

Value

The combined cowplot::plot_grid() object is returned invisibly. The PDF is always written to output.dir.

See also

unmixed.nxn.plot(), create.biplot()