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##
## BioCro/R/plotAQ.R by Fernando Ezequiel Miguez Copyright (C) 2007-2009
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 or 3 of the License
## (at your option).
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## A copy of the GNU General Public License is available at
## http://www.r-project.org/Licenses/
##
##
## helper plotting functions
## Function to plot A/Q curves
##
## data are assumed to have
##
## col 1: trt
## col 2 (optional): other treatment factor
## col 2: Assimilation
## col 3: Quantum flux
## col 4: Temperature
## col 5: Relative humidity
## col 6 (optional): Reference CO2
plotAQ <- function(data,fittd,
id.col=1,
trt.col=2,
ylab="CO2 Uptake",
xlab="Quantum flux",
by=c("trt","ID"),type="o",...){
by <- match.arg(by)
Acol <- trt.col + 1
Qp.col <- trt.col + 2
if(missing(fittd) || is.null(fittd)){
if(by == "trt"){
plot1 <- xyplot(data[,Acol] ~ data[,Qp.col] | factor(data[,trt.col]),
ylab = ylab,
xlab = xlab,
type = type, ...)
plot(plot1)
}else{
plot1 <- xyplot(data[,Acol] ~ data[,Qp.col] | factor(data[,id.col]),
ylab = ylab,
xlab = xlab,
type = type, ...)
plot(plot1)
}
}else{
stopifnot(length(fittd) == nrow(data))
if(by == "trt"){
plot1 <- xyplot(data[,Acol] + fittd ~ data[,Qp.col] | factor(data[,trt.col]),
ylab = ylab,
xlab = xlab,
type = type, ...)
plot(plot1)
}else{
plot1 <- xyplot(data[,Acol] + fittd ~ data[,Qp.col] | factor(data[,id.col]),
ylab = ylab,
xlab = xlab,
type = type, ...)
plot(plot1)
}
}
}
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