Skip to contents

Create Biplot

Source: R/create_biplot.R
create.biplot.Rd

Create Biplot

Usage

create.biplot(
  plot.data,
  x.dim,
  y.dim,
  asp,
  variants = NULL,
  spread.kappa = 2,
  x.lab = NULL,
  y.lab = NULL,
  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",
  save = TRUE,
  title = NULL,
  output.dir = NULL,
  width = 5,
  height = 5
)

Arguments

plot.data

A matrix or dataframe containing the flow cytometry data to be plotted. Column names should match the dimensions specified by x.dim and y.dim.

x.dim

String specifying the column of plot.data for the x-axis of the plot.

y.dim

String specifying the column of plot.data for the y-axis of the plot.

asp

The AutoSpectral parameter list.

variants

The variant list returned by get.spectral.variants(). When supplied, red curves are drawn for whichever of x.dim/y.dim variants$thresholds covers: each channel's flat threshold (variants$thresholds) plus spread.kappa spread standard deviations from the other axis's own spillover into it (variants$spillover.spread), and, below zero, the same spread widening subtracted from the directly measured negative-tail flat threshold (variants$neg.thresholds) rather than mirrored from the positive curve about zero. Falls back to the mirrored positive threshold, with a warning, when variants$neg.thresholds is absent (an older cached variants object). This is the one-source restriction of get.spread.thresholds()'s formula to whichever fluorophore the other axis actually shows - contributions from every other fluorophore in the panel are not visualisable on a 2D plot and are not included. NULL (default) draws no reference curves.

spread.kappa

Numeric, spread standard deviations allowed above the flat threshold when variants is supplied - see get.spread.thresholds(). Default 2.

x.lab

An optional label for the x-axis. If none is given (default NULL), the column name specified by x.dim will be used.

y.lab

An optional label for the y-axis. If none is given (default NULL), the column name specified by y.dim will be used.

x.min

Minimum value for the x-axis. Default is -5000.

x.max

Maximum value for the x-axis. Default is the value specified by asp$expr.data.max, which will be the maximum for the cytometer.

y.min

Minimum value for the y-axis. Default is -5000.

y.max

Maximum value for the y-axis. Default is the value specified by asp$expr.data.max, which will be the maximum for the cytometer.

x.width.basis

Width basis for the biexponential transform for the x-axis. Default is -1000.

y.width.basis

Width basis for the biexponential transform for the x-axis. Default is -1000.

max.points

Number of points to plot (speeds up plotting). Default is 5e6.

color.palette

Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is rainbow, which will be similar to FlowJo or SpectroFlo. Other pptions are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.

save

Logical, if TRUE, saves a JPEG file to the output.dir. Otherwise, the plot will simply be created in the Viewer.

title

Optional title for the plot filename. If NULL, defaults to x.lab vs. y.lab.

output.dir

Optional output directory. Default is NULL, in which case the current working directory will be used.

width

Numeric, width of the saved plot. Default is 5.

height

Numeric, height of the saved plot. Default is 5.

Value

Creates a biplot in the Viewer and optionally saves it as a JPEG file.