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

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

Description

produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.

Usage

ggpairsDens(flowfile, channels = NULL, group = NULL, notToPlot = NULL, ...)

Arguments

flowfile	flowframe to be plotted
channels	a character vector of length 2 or more. It must contain channel names in the flowfile.
group	cluster groups. It must be equal to the number of particles in the flowfile. If group is null cluster boundaries are not drawn.
notToPlot	columns not to plot. This is especially useful for for plotting all columns in a
...	not used at the moment @return a ggplot object

Value

a ggplot object

Examples

 # example without clustering
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 <- lnTrans(x = flowfile_noneg, c('SSC.W', 'TIME'))
ggpairsDens(flowfile = flowfile_logtrans,
            channels = c("FSC.HLin", "RED.R.HLin", "RED.B.HLin", 
            "NIR.R.HLin"))

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