A method for visualizing annular points that a user (or users) selected on a calcified structure is described in this vignette. This vignette assumes that you have an R data file or files created from selecting points on a calcified structure using
digitizeRadii() as described in the Collecting Radial Measurements vignette. It also assumes that you understand the language and functions introducted in that vignette.
This vignette will use the following R data files:
digitizeRadii("Oto140306.jpg",id="140306",reading="DHO", description="Used to demonstrate use of scale-bar.", scaleBar=TRUE,scaleBarLength=1,edgeIsAnnulus=TRUE, windowSize=12)
RFishBC package is needed for this vignette.
The plotting character, color, and relative size of the selected points may be changed with
cex.show=, respectively. By default, the points are connected which will display as a linear transect if
makeTransect=TRUE (the default) was used when selecting annuli in
digitizeRadii(). The color and width of the connected lines may be changed with
lwd.connect=. The connected lines may be excluded altogether with
connect=FALSE. Annuli will be numbered if
showAnnuliLabels=TRUE (the default) with label colors and relative size changed with
cex.ann=, respectively. Annuli for which numbers are plotted may be controlled with
annuliLabels= (e.g., only the first six plus several others after that are shown for the Kiyi otolith below). Defaults for all of these arguments may be set with
RFBCoptions() as was demonstrated in the Setting Arguments section of this vignette
showDigitizedImage("Oto140306_DHO.rds",pch.show="+",col.show="blue", col.connect="white",col.ann="black",cex.ann=1, annuliLabels=c(1:6,8,10,13))
In some instances, you may be interested in visually comparing the selected points from multiple readings of the same structure. The
showDigitizedImage() function can accomplish this if it is given a vector of R data file names created from the same structure.
listFiles() function (described in the Collecting Radial Measurements vignette) may be used to identify all filenames in the current working directory that have the file extension given in the first argument. For example, all files with the “rds” extension are found below.
listFiles("rds") #>  "Oto140306_DHO.rds" "Oto140306_OHD.rds" "Scale_1_DHO.rds" #>  "Scale_1_ODH.rds" "Scale_1_OHD.rds" "Scale_2_DHO.rds" #>  "Scale_3_DHO.rds"
This list of names can be further filtered by including other key words for the filenames in
other=. For example, all files with the “rds” extension that contain the keyword “Scale_1” are returned below. For our purposes here, these filenames are saved into an object (e.g.,
( fns <- listFiles("rds",other="Scale_1") ) #>  "Scale_1_DHO.rds" "Scale_1_ODH.rds" "Scale_1_OHD.rds"
Aspects of the connecting lines and points may be controlled with arguments to
showDigitizedData(). For example, the code below uses different colors for each set of connecting lines and points.