spectralplot: Load data, choose a style, and choose output method

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

Load data, choose a style, and choose output method

Description

This function loads a flowFrame of flowSet and invokes the plotting function. 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

spectralplot(
  flowfile,
  theme = "viridis",
  save = FALSE,
  bins = 512,
  normalize = FALSE,
  params = NULL,
  guessPop = FALSE,
  unstained = NULL
)

Arguments

flowfile	A flowSet or flowFrame.
theme	Choose a theme: 'viridis' (default), 'bigfoot', or 'aurora'.
save	FALSE: in console (default). 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 (default).
params	Specify parameters (in order) to plot. If NULL (default), 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.
unstained	flowFrame of the negative data, only needed if guessPop = TRUE

Value

Images of full spectrum

Author(s)

Christopher Hall, Babraham Institute

See Also

spectralplottingtool

Examples

## flowSpectrum has one demo file that can be loaded.  
ff <- read.FCS(system.file("extdata", "PE.fcs", package = "flowSpectrum"))

## create plots using spectralplot().
spectralplot(ff, theme='viridis', save=FALSE, bins=512, normalize=FALSE, params=NULL)

## load flowSet and run spectralPlot()
fs <- read.flowSet(list.files('C:/Users/Chris/testspectra', full.names = TRUE))
spectralPlot(fs)

## If the parameters are out of order, or you want a custom order, you need to create a character vector
params <- grep("-W|-H|Time|SC",ff@parameters@data$name,value = TRUE, invert=TRUE)

## If the spectra is "unclean"
spectralPlot(fs, guessPop = TRUE, normalize = TRUE)

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