plotCytogram: Plot a Phytoplankton Cytogram

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

Plot a Phytoplankton Cytogram

Usage

plotCytogram(df, x.ax, y.ax, add.legend=FALSE, pop.def=POP.DEF, transform=TRUE, cex=0.5, pch=16, xlab = x.ax, ylab = y.ax, ...)

Arguments

df	a dataframe of events (rows) and channels (columns).
x.ax	column to plot in the x.axis
y.ax	column to plot in the y.axis
add.legend	should the plot automatically generate a legend
pop.def	A population (rows) definition dataframe with parameters (columns) for gating and clustersing.
transform	plot Log transform data, if appropriate
cex	character expansion for the points. Undefined background points are 1/3rd of the foreground points.
pch	point character
xlab	label for the x axis. by default equals x.ax
ylab	label for the y axis. by default equals y.ax
...	other paramters passed to plot

Value

a cytogram plot

Examples

opp.file.path <- system.file("extdata","seaflow_cruise","2011_001", "1.evt.opp", 
			package="flowPhyto")
pop.file.path <- system.file("extdata","seaflow_cruise","pop.def.tab", 
			package="flowPhyto")

opp <- readSeaflow(opp.file.path)
def <- readPopDef(pop.file.path)
pop <- classify(x=opp, pop.def= def)

# Visualize the result of Classify using the function plotCytogram()
plotCytogram(pop, "fsc_small","chl_small", pop.def= def)

armbrustlab/flowPhyto documentation built on May 10, 2019, 1:40 p.m.