pairsPlot: produces a scatter plot of the expression matrix of a...

In fomotis/cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

Description

produces a scatter plot of the expression matrix of a flowframe. Note that, it takes some time to display the plot.

Usage

pairsPlot(x, notToPlot = c("TIME"), ...)

Arguments

x	flowframe to be plotted
notToPlot	column in expression matrix not to be plotted
...	other arguments. Not used at the moment

Value

a plot object

Examples

flowfile_path <- system.file("extdata", "B4_18_1.fcs", 
              package = "cyanoFilter",
              mustWork = TRUE)
flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE,
                               transformation = FALSE, emptyValue = FALSE,
                               dataset = 1) 
flowfile_nona <- cyanoFilter::noNA(x = flowfile)
flowfile_noneg <- cyanoFilter::noNeg(x = flowfile_nona)
flowfile_logtrans <- cyanoFilter::lnTrans(x = flowfile_noneg, 
                      c('SSC.W', 'TIME'))
pairsPlot(flowfile_logtrans,
           notToPlot = c("TIME", "SSC.W",
           "SSC.HLin", "NIR.R.HLin", 
           "FSC.HLin"))  
           

fomotis/cyanoFilter documentation built on Aug. 1, 2021, 10:58 p.m.