plotCruiseStats: Plot a seaflow cruise statistics

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

Read in the pop.stats.tab file and plot maps, or line plots of it and optionall sds info

Usage

plotCruiseStats(cruise, x.var='map', y.vars=c('conc','chl_small','fsc_small'), 
		pops= c("ultra", "synecho"), sds.var=NULL,
		date.range=as.POSIXct(c("2009-01-01", "2099-12-31"), tz='UTC'), 
		output.path=paste(REPO.PATH, cruise,'/plots/',sep=''), ...)

Arguments

cruise	Simplified cruise name (same name as the subdirectory in the seaflow data dir).
x.var	X variable: Either map or lat, long or time.
y.vars	Y variables: either conc, fluor, or fsc.
pops	Which populattions to plot. See the pop datastructure for abreviations to use.
sds.var	Which of the sds variables to plot as a secondary axis in a line plot.
date.range	date range.
output.path	Path to the directory where you wish to output data.
...	Additional parameters passed to plot.

Value

an overview statistics plot file is output to disk

Examples

cruise <- system.file("extdata","seaflow_cruise", package="flowPhyto")

plotCruiseStats(cruise=cruise, output.path='.')

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