ggpairsDens {cyanoFilter} | R Documentation |
produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.
ggpairsDens(flowfile, channels = NULL, group = NULL, notToPlot = NULL, ...)
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 |
a ggplot object
# 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"))