reinstitute plotting of lists

While updating line calculation code the lapply wrapper in circleplot()
was removed, withdrawing capacity to plot multiple objects stored in
lists. This has been re-added in the current version. Functions
make.wide.format and make.long.format no longer available to user, but
are given in sppairs [devtools::install_github(‘mjwestgate/sppairs)].

Author: mjwestgate

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: circleplot
-Version: 0.4
+Version: 0.4.1
 Date: 2016-02-03
 Title: Circular plots of distance and association matrices
 Author: Martin J. Westgate <martinjwestgate@gmail.com>

INDEX

@@ -1,6 +1,4 @@
 circleplot	Draw a plot
 draw.circle	Add a circle to an existing plot
 make.circle	Return a set of points on the circumference of a circle
-make.long.format	Convert a matrix to a data.frame
-make.wide.format	Convert a data.frame to a matrix
 point.attr	Generate point colours

NAMESPACE

@@ -1 +1 @@
-export(circleplot, draw.circle, make.circle, make.long.format, make.wide.format, point.attr)
+export(circleplot, draw.circle, make.circle, point.attr)

R/plot_calls.R

@@ -29,40 +29,44 @@ circleplot<-function(
 	scale.distance<-as.matrix(scale.distance)
 
 	# set plot window attributes
-	if(add==FALSE){
-		do.call(par, circleplot.object$par)
-		do.call(plot, circleplot.object$plot)}
 	if(class(input)=="list")par(mfrow=panel.dims(length(circleplot.object$lines)))
-
-	# loop to calculate lines of requisite location and colour
-	line.data<-circleplot.object$lines[[1]]
-	line.list<-split(line.data, c(1:nrow(line.data)))
-	line.list<-lapply(line.list, function(x, plot.object, distance, options){
-		calc.lines(x, plot.object, distance, options)},
-		plot.object=circleplot.object, distance=scale.distance, options= plot.options)
-
-	# draw these lines
-	invisible(lapply(line.list, 
-		FUN=function(z, asymmetric, arrow.attr){
-			draw.curves(z)
-			if(asymmetric)draw.arrows(z, arrow.attr)},
-		asymmetric=attr(circleplot.object, "asymmetric"), arrow.attr=plot.options$arrows))
-
-	# add points or polygons, depending on style
-	switch(style,
-	"classic"={do.call(points, 
-		as.list(circleplot.object$points[, -which(colnames(circleplot.object$points)=="labels")]))},
-	"pie"={invisible(lapply(circleplot.object$polygons, function(x){do.call(polygon, x)}))},
-	"clock"={
-		invisible(lapply(circleplot.object$nodes, function(x){do.call(lines, x)}))
-		do.call(draw.circle, plot.options$border[-which(names(plot.options$border)=="tcl")])}
-	)
-
-	# label points
-	label.suppress.test<-is.logical(plot.options$point.labels) & length(plot.options$point.labels)==1
-	if(label.suppress.test==FALSE){
-		labels.list<-split(circleplot.object$labels, 1:nrow(circleplot.object$labels))
-		invisible(lapply(labels.list, FUN=function(x){do.call(text, x)}))}
+	
+	invisible(lapply(circleplot.object$lines, function(a, add, circleplot.object, scale.distance, plot.options){
+		if(add==FALSE){
+			do.call(par, circleplot.object$par)
+			do.call(plot, circleplot.object$plot)}
+	
+		# loop to calculate lines of requisite location and colour
+		# line.data<-circleplot.object$lines[[1]]
+		line.list<-split(a, c(1:nrow(a)))
+		line.list<-lapply(line.list, function(x, plot.object, distance, options){
+			calc.lines(x, plot.object, distance, options)},
+			plot.object=circleplot.object, distance=scale.distance, options= plot.options)
+	
+		# draw these lines
+		invisible(lapply(line.list, 
+			FUN=function(z, asymmetric, arrow.attr){
+				draw.curves(z)
+				if(asymmetric)draw.arrows(z, arrow.attr)},
+			asymmetric=attr(circleplot.object, "asymmetric"), arrow.attr=plot.options$arrows))
+	
+		# add points or polygons, depending on style
+		switch(style,
+		"classic"={do.call(points, 
+			as.list(circleplot.object$points[, -which(colnames(circleplot.object$points)=="labels")]))},
+		"pie"={invisible(lapply(circleplot.object$polygons, function(x){do.call(polygon, x)}))},
+		"clock"={
+			invisible(lapply(circleplot.object$nodes, function(x){do.call(lines, x)}))
+			do.call(draw.circle, plot.options$border[-which(names(plot.options$border)=="tcl")])}
+		)
+	
+		# label points
+		label.suppress.test<-is.logical(plot.options$point.labels) & length(plot.options$point.labels)==1
+		if(label.suppress.test==FALSE){
+			labels.list<-split(circleplot.object$labels, 1:nrow(circleplot.object$labels))
+			invisible(lapply(labels.list, FUN=function(x){do.call(text, x)}))}
+		
+	}, add=add, circleplot.object= circleplot.object, scale.distance= scale.distance, plot.options= plot.options))
 
 	if(class(input)=="list")par(mfrow=c(1, 1))
 

R/prep_objects.R

@@ -446,7 +446,12 @@ calc.circleplot<-function(x, plot.options, cluster, style){
 	# get information on points and labels, but do not add x,y coordinates
 	point.dframe<-plot.options$points
 	point.dframe$order.auto<-new.order
-	label.dframe<-plot.options$point.labels
+	if(class(plot.options$point.labels)=="logical"){
+		if(length(plot.options$point.labels)==1){
+			label.dframe<-point.dframe
+			label.dframe$cex<-0}
+	}else{
+		label.dframe<-plot.options$point.labels}
 
 	# reorder as necessary
 	if(any(grepl("order", colnames(point.dframe)))){