ggplotDens2: plots two channels of a flowframe with different colors for...

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

Description

plots two channels of a flowframe with different colors for clusters identified.

Usage

ggplotDens2(flowfile, channels, group, ...)

Arguments

flowfile	flowframe to be plotted
channels	a character vector of length 2, must contain channel names in the flowfile.
group	cluster groups. must be equal to the number of particles in the flow cytometer.
...	not used at the moment

Value

a ggplot 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'))
cells_nonmargin <- cellMargin(flowframe = flowfile_logtrans, 
                              Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
cells_nodebris <- debrisNc(flowframe = reducedFlowframe(cells_nonmargin),
                            ch_chlorophyll = "RED.B.HLin",
                            ch_p2 = "YEL.B.HLin",
                            ph = 0.05)
cct <- phytoFilter(flowfile = reducedFlowframe(cells_nodebris),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))
ggplotDens2(reducedFlowframe(cct), 
c("RED.B.HLin", "YEL.B.HLin"),
group = "Clusters")

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