ggtern 1.0.3.2

Author: Nicholas Hamilton

.DS_Store

@@ -2,7 +2,7 @@ Package: ggtern
 Type: Package
 Title: An extension to ggplot2, for the creation of ternary diagrams.
 Version: 1.0.3.2
-Date: 2014-01-30
+Date: 2014-05-30
 Author: Nicholas Hamilton <[email protected]>
 Maintainer: Nicholas Hamilton <[email protected]>
 Description: ggtern is a package that extends the functionality of ggplot2, giving the capability to plot ternary diagrams for (subset of) the ggplot2 geometries. Additionally, ggtern has implemented several NEW geometries which are unavailable to the standard ggplot2 release. For further examples and documentation, please proceed to the ggtern website. 

DESCRIPTION

@@ -15,7 +15,6 @@ export("%+%")
 export("%+replace%")
 export(arrow)
 export(element_ternary)
-export(geom_smooth)
 export(ggplot_build)
 export(ggtern)
 export(ifthenelse)
@@ -31,6 +30,7 @@ export(scale_R_continuous)
 export(scale_T_continuous)
 export(stat_density2d)
 export(geom_density2d)
+export(geom_smooth)
 export(geom_confidence)
 export(geom_errorbarT)
 export(geom_errorbarL)

NAMESPACE

@@ -5,23 +5,23 @@
 #' 
 #' This can be useful for dealing with overplotting. Additional weight aesthetic (see aesthetic section below) permits better weighting if desired
 #'
-#' @aliases Density2dTern
+#' @aliases Density2dTern GeomDensity2dtern
 #' @section Aesthetics: 
 #' \Sexpr[results=rd,stage=build]{ggtern:::rd_aesthetics("geom", "density2dtern")}
 #' @inheritParams ggplot2::geom_point
 #' @inheritParams ggplot2::geom_path
-#' @aliases GeomDensity2dtern
 #' @export
-geom_density2d <- function (mapping = NULL, data = NULL, stat = "Density2dtern", position = "identity",
-                            lineend = "butt", linejoin = "round", linemitre = 1, na.rm = FALSE, ...) { 
+geom_density2d <- function (mapping = NULL, data = NULL, stat = "auto", position = "identity",
+                            lineend = "butt", linejoin = "round", linemitre = 1, na.rm = FALSE, ...){
+  if(stat == 'auto') stat = iflasttern('density2dtern','density2d')
   GeomDensity2dtern$new(mapping = mapping, data = data, stat = stat, position = position, 
                     lineend = lineend, linejoin = linejoin, linemitre = linemitre, na.rm = na.rm,...)
 }
 
 GeomDensity2dtern <- proto(ggint$GeomPath,{
   objname <- "density2dtern"
-  #draw <- function(., data, scales, coordinates, arrow = NULL, lineend = "butt", linejoin = "round", linemitre = 1, ..., na.rm = FALSE)
-  #  GeomConfidence$draw(.=.,data=data,scales=scales,coordinates=coordinates,lineend = lineend,na.rm = na.rm,...)
   default_stat <- function(.) StatDensity2dtern
   default_aes <- function(.) aes(colour="#3366FF", size = 0.5, linetype = 1, alpha = NA,weight=NULL,fill="transparent")
+  #draw <- function(., data, scales, coordinates, arrow = NULL, lineend = "butt", linejoin = "round", linemitre = 1, ..., na.rm = FALSE)
+  #  GeomConfidence$draw(.=.,data=data,scales=scales,coordinates=coordinates,lineend = lineend,na.rm = na.rm,...)
 })

R/.DS_Store

@@ -70,8 +70,8 @@ ggint$GeomSegment <- proto(Geom, {
     pieces <- pieces[order(pieces$group),]
     GeomPath$draw_groups(pieces, scales, coordinates, arrow = arrow, ...)
   }
-  default_stat <- function(.) StatIdentity
   required_aes <- c("x", "y")
+  default_stat <- function(.) StatIdentity
   default_aes <- function(.) aes(colour="black", size=0.5, linetype=1, alpha = NA)
   guide_geom <- function(.) "path"
 })

R/geom-density2d.R

@@ -12,8 +12,7 @@
 #' @param filename file name/filename of plot
 #' @param plot plot to save, defaults to last plot displayed
 #' @param device device to use, automatically extract from file name extension
-#' @param path path to save plot to (if you just want to set path and not
-#'    filename)
+#' @param path path to save plot to (if you just want to set path and not filename)
 #' @param scale scaling factor
 #' @param width width (defaults to the width of current plotting window)
 #' @param height height (defaults to the height of current plotting window)
@@ -29,11 +28,10 @@
 #' plot <- ggtern(data=Feldspar,aes(An,Ab,Or)) + geom_point() + theme_rgbw()
 #' ggsave(plot,filename='test.png')
 #' }
-ggsave <- function(filename = default_name(plot), plot = last_plot(),
+ggsave <- function(filename = default_name(), plot = last_plot(),
                    device = default_device(filename), path = NULL, scale = 1,
                    width = par("din")[1], height = par("din")[2], units = c("in", "cm", "mm"),
                    dpi = 300, limitsize = TRUE, ...) {
-  
   if (!inherits(plot, "ggplot")) stop("plot should be a ggplot2 plot")
 
   eps <- ps <- function(..., width, height)  
@@ -49,7 +47,6 @@ ggsave <- function(filename = default_name(plot), plot = last_plot(),
     grDevices::win.metafile(..., width=width, height=height)
   emf <- function(..., width, height)
     grDevices::win.metafile(..., width=width, height=height)
-  
   png <- function(..., width, height) 
     grDevices::png(...,  width=width, height=height, res = dpi, units = "in")
   jpg <- jpeg <- function(..., width, height) 
@@ -59,10 +56,15 @@ ggsave <- function(filename = default_name(plot), plot = last_plot(),
   tiff <- function(..., width, height) 
     grDevices::tiff(..., width=width, height=height, res = dpi, units = "in")
 
-  default_name <- function(plot) { 
-    paste(ggtern:::ggint$digest.ggplot(plot), ".pdf", sep="")
+  default_name <- function(){
+    filename="plot"
+    suffix = NULL
+    while(file.exists(paste(filename,suffix,".pdf",sep=""))){
+      if(is.null(suffix)) suffix = 0
+      else suffix = suffix + 1
+    }
+    paste(filename,suffix,".pdf",sep="")
   }
-  
   default_device <- function(filename) {
     pieces <- strsplit(filename, "\\.")[[1]]
     ext <- tolower(pieces[length(pieces)])
@@ -116,6 +118,4 @@ ggsave <- function(filename = default_name(plot), plot = last_plot(),
   print(plot)
 
   invisible()
-}
-
-#body(ggsave)[[which(as.list(body(ggsave)) == 'print(plot)')]] <- substitute(ggtern::print.ggtern(plot))
+}

R/geom-segment.R

@@ -17,9 +17,11 @@
 
 #' \code{get_last_coord} is a function that returns the last coordinate system used.
 #' @rdname undocumented
+#' @keywords internal
 get_last_coord <- .coordinates$get
 
 #' \code{set_last_coord} set the last coordinate system.
 #' @param new the coordinate system to set
 #' @rdname undocumented
+#' @keywords internal
 set_last_coord <- .coordinates$set

R/ggsave.R

@@ -7,7 +7,8 @@
 #' @aliases StatDensity2dtern
 #' @export
 #' @seealso \code{\link[ggtern]{geom_density2d}}
-stat_density2d <- function (mapping = NULL, data = NULL, geom = "density2dtern", position = "identity", na.rm = FALSE, contour = TRUE, n = 100, ...) {
+stat_density2d <- function (mapping = NULL, data = NULL, geom = "auto", position = "identity", na.rm = FALSE, contour = TRUE, n = 100, ...) {
+  if(geom == 'auto') geom = iflasttern('density2dtern','density2d')
   StatDensity2dtern$new(mapping = mapping, data = data,geom=geom,geometry=geom,position = position, na.rm = na.rm, contour = contour, n = n,...)
 }
 

R/global.R

@@ -3,6 +3,7 @@
                  segment   = "segment",
                  polygon   = "polygon",
                  text      = "text",
+                 contour   = "contourtern",
                  density2d = "density2dtern",
                  smooth    = "smoothtern",
                  rug       = "rug",