archigrow(inputlie, inputtps, res=NULL, unitlength="px", unittime, unitangle="d", rotation=0, numdate=NULL, finalscale=NULL, coldyn, GRscale=NULL, main=NULL, xlab=NULL, ylab=NULL, xlim=NULL, ylim=NULL, ...)inputtps.inputlie.unitlength="mm" or unitlength="cm".unitangle) that must be used by the function to perform a clockwise rotation of the root system (see details).is.null(numdate)=FALSE. If TRUE, the root system architecture at the selected observation dates will be plotted with the same X and Y-axis scales to that used to draw the root system architecture at the last observation date. If FALSE, the root system architecture at each observation date will be plotted using different X and Y-axis ranges of coordinates (xlim and ylim).archigrow interpolates the colour(s) contained in coldyn between the minimum and the maximum values of the computed standardized growth rate matrix (if is.null(GRscale)=TRUE) or between min(GRscale) and max(GRscale) (if is.null(GRscale)=FALSE).unitlength/unittime) that must be used by the function to plot each vectorized root system.is.null(main)=TRUE, the default title for each plot is the name of the corresponding lie file.is.null(xlab)=TRUE, the default label for the X axis is X (unitlength).is.null(ylab)=TRUE, the default label for the Y axis is Y (unitlength).unitlength.unitlength.unitlength/unittime).Returns a X-Y plot for each vectorized root system located in inputlie.
archigrow allows the X-Y plotting of vectorized root systems for selected observation dates with a colour code depending on the growth rate value of each link constituting the vectorized root systems. The archigrow function will successively locate and read the lie and tps files created by DART, compute a growth rate matrix and plot the vectorization results at selected observation dates for each analysed root system. First, archigrow will check if all arguments have been written in the suitable mode. If res and rotation are specified, the function will check if the numeric values required by these arguments are positive. If is.null(numdate)=FALSE, the function will also automatically check if the numeric values in numdate are positive and sorted by increasing values. If an error occurs for one argument, the code stops and the corresponding error message will be returned by the function. Second, the function will use inputlie and inputtps to locate and read the raw lie and tps files created by DART. To run archigrow efficiently, DART files must have been saved with their appropriate extensions (.lie or .tps). If inputtps contains a single tps file, it will be used by archigrow for each lie file located in inputlie. If inputps contains more than one tps file, the number of tps files in inputtps must be equal to the number of lie files in inputlie and corresponding lie and tps files must have the same name. If an error occurs at this step, a message will be returned by the function. Third, archigrow will compute a growth rate matrix containing for each root constituting the vectorized root system its corresponding growth rate value at each observation date. Finally, archigrow will plot each vectorized root system located in inputlie at the observation dates specified by numdate. By default (when is.null(numdate)=TRUE), only the root system architecture at the last observation date will be plotted. If is.null(numdate)=FALSE, archigrow will plot only the root system architecture for the selected observation dates.
Due to technical limitations, it is sometimes easier to take a picture of a root system if it is rotated before image acquisition. In this case, the vectorized root system will depict a rotation compared with the natural plant root system. To make a correction, one can use rotation to specify an angle value expressed in unitangle that will be used by the function to rotate the vectorized root system clockwise before plotting and root system architecture parameters calculation.
Additional graphical parameters can also be used to personalize the graphical outputs (see par). By default, a legend showing the colour gradient used to draw each vectorized root system is shown at the right side of the final plot.
Growth rates are calculated as follows:
Le Bot J., Serra V., Fabre J., Draye X., Adamowicz S., Pages L. (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, DOI: 10.1007/s11104-009-0005-2.
par.
## Importation of example datasets
data(ch7lie)
data(ch7tps)
## Creation of a folder (DART_archigrow) inside a temporary directory to contain the lie and tps
## example datasets created by DART
dirDART <- paste(tempdir(), "/DART_archigrow", sep="")
dir.create(dirDART)
## Definition of the number of lie and tps files that will be saved inside dirDART
n <- 1
## Creation of lie and tps files inside dirDART
for (i in 1:n) {
write.table(ch7lie, file=paste(dirDART,"/ch7_",i,".lie", sep=""), row.names=FALSE)
write.table(ch7tps, file=paste(dirDART,"/ch7_",i,".tps", sep=""), row.names=FALSE)}
## Use of archigrow to plot the root system architecture for selected observation dates
## Use the same X and Y-axis scales to that used for the last observation date
ch7_output_1 <- archigrow(inputlie=dirDART, inputtps=dirDART, res=75, unitlength="cm",
unittime="day", coldyn=c("blue", "orange", "red"), numdate=c(15,30), finalscale=TRUE,
las=1, bty="l", asp=1, xaxp=c(0,30,3), lwd=2)
unlink(dirDART, recursive=TRUE)
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