spectralplottingtool: Plotting function to output PNG or an R object of the...

In hally166/flowSpectrum: Creates flow cytometry spectral plots from the Aurora, Bigfoot and ID7000

Plotting function to output PNG or an R object of the spectrum.

Description

Can be wrapped in the data loading function, or directly with a flowFrame or inside fsApply() for a flowSet. This function tidies the fcs data from a flowFrame or flowSet. Choose a theme: 'viridis', 'bigfoot', or 'aurora'. Viridis is colourblind accessible. Choose to save to the working directory or display in current session. Choose the number of bins (granularity) of the data. You can normalize to the max median signal for "clean" files. If you misspell an option it will give an error.

Usage

spectralplottingtool(
  flowfile,
  theme,
  save,
  bins,
  normalize,
  params,
  guessPop,
  unstained
)

Arguments

flowfile	A flowSet or flowFrame.
theme	Choose a theme: 'viridis', 'bigfoot', or 'aurora'.
save	FALSE: in console. TRUE : as png file in working directory.
bins	Choose the granularity of the data. Between 200 and 1000 works well for most data.
normalize	Normalize the data to the max median signal (only for clean signals). TRUE or FALSE
params	Specify parameters (in order) to plot. Parameters will be selected based on the cytometer model.
guessPop	Try to select only the positive spectral signal (200 events). It is recommend to set normalize to TRUE when using guessPop.

Value

Images of full spectrum

Author(s)

Christopher Hall, Babraham Institute

See Also

spectralplot

hally166/flowSpectrum documentation built on May 14, 2023, 3:21 p.m.