R/plotAC.R

In serbinsh/biocro: Simulation of Energycane and Sugarcane

## /R/plotAC.R by Fernando Ezequiel Miguez Copyright (C) 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/
## 
## Function to plot A/Ci 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:
## Intercellular CO2 col 7: Reference CO2
##' Plotting function for A/Ci curves
##'
##' A small helper function that can be used to easily plot multiple A/Ci
##' curves
##'
##'
##' @param data Input data in the format needed for the
##' \code{\link{mOpc4photo}}.
##' @param fittd Optional fitted values.
##' @param id.col Specify which column has the ids. Default is col 1.
##' @param trt.col Specify which column has the treatments. Default is col 2.
##' If no treatment is specified then use 1.
##' @param ylab Label for the y-axis.
##' @param xlab Label for the x-axis.
##' @param by Whether to plot by id or by treatment.
##' @param type this argument is passed to the \code{\link{xyplot}}. It changes
##' the plotting symbols behavior.
##' @export
##' @return NULL %% ~Describe the value returned %% If it is a LIST, use %%
##' \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of
##' 'comp2'} %% ...
##' @author Fernando E. Miguez
##' @seealso See Also \code{\link{xyplot}}.
##' @keywords hplot
##' @examples
##'
##' data(aci)
##' plotAC(aci, trt.col=1)
##'
##'
plotAC <- function(data, fittd, id.col = 1, trt.col = 2, ylab = "CO2 Uptake", xlab = "Ci", 
    by = c("trt", "ID"), type = c("p", "smooth")) {
    by <- match.arg(by)
    Acol <- trt.col + 1
    Ci.col <- trt.col + 5
    if (missing(fittd) || is.null(fittd)) {
        if (by == "trt") {
            plot1 <- xyplot(data[, Acol] ~ data[, Ci.col] | factor(data[, trt.col]), 
                ylab = ylab, type = type, xlab = xlab)
            plot(plot1)
        } else {
            plot1 <- xyplot(data[, Acol] ~ data[, Ci.col] | factor(data[, id.col]), 
                ylab = ylab, type = type, xlab = xlab)
            plot(plot1)
        }
    } else {
        stopifnot(length(fittd) == nrow(data))
        if (by == "trt") {
            plot1 <- xyplot(data[, Acol] + fittd ~ data[, Ci.col] | factor(data[, 
                trt.col]), ylab = ylab, type = type, xlab = xlab)
            plot(plot1)
        } else {
            plot1 <- xyplot(data[, Acol] + fittd ~ data[, Ci.col] | factor(data[, 
                id.col]), ylab = ylab, type = type, xlab = xlab)
            plot(plot1)
        }
    }
}