merged to 0.5.3

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ggbeeswarm
 Type: Package
 Title: Categorical Scatter (Violin Point) Plots
-Version: 0.5.2
-Date: 2016-11-30
+Version: 0.5.3
+Date: 2016-12-01
 Authors@R: c(
     person(given="Erik", family="Clarke", role=c("aut", "cre"), email="erikclarke@gmail.com"),
     person(given="Scott", family="Sherrill-Mix", role=c("aut"), email="sherrillmix@gmail.com"))

R/geom-beeswarm.R

@@ -31,11 +31,10 @@ geom_beeswarm <- function(
   mapping = NULL,
   data = NULL,
   priority = c("ascending", "descending", "density", "random", "none"),
-  cex=2,
+  cex=1,
   groupOnX=NULL,
   dodge.width=0,
   stat='identity',
-  position = "quasirandom",
   na.rm = FALSE,
   show.legend = NA,
   inherit.aes = TRUE,

R/position-beeswarm.R

@@ -20,7 +20,7 @@
 #'   ggplot2::qplot(variable, value, data = distro) +
 #'     geom_beeswarm(priority='density',cex=2.5)
 #'
-position_beeswarm <- function (priority = c("ascending", "descending", "density", "random", "none"),cex=2,groupOnX=NULL,dodge.width=0){
+position_beeswarm <- function (priority = c("ascending", "descending", "density", "random", "none"),cex=1,groupOnX=NULL,dodge.width=0){
   ggplot2::ggproto(NULL,PositionBeeswarm,priority = priority,cex=cex,groupOnX=NULL,dodge.width=dodge.width)
 }
 
@@ -61,13 +61,38 @@ PositionBeeswarm <- ggplot2::ggproto("PositionBeeswarm",ggplot2:::Position, requ
     trans_x<-NULL
     trans_y<-NULL
 
+    getScaleDiff<-function(scales){
+      if(is.null(scales$limits))lims<-scales$range$range
+      else lims<-scales$limits
+      if(inherits(scales,'ScaleContinuous')){
+        limDiff<-diff(lims)
+      }else if(inherits(scales,'ScaleDiscrete')){
+        limDiff<-length(unique(lims))
+      }else{
+        stop('Unknown scale type')
+      }
+      if(limDiff==0)limDiff<-1
+      return(limDiff)
+    }
+
     trans_xy <- function(xx){
+      xRange<-getScaleDiff(scales$x)
+      yRange<-getScaleDiff(scales$y)
       newX<-ave(
         data[,ifelse(params$groupOnX,'y','x')],
         data[,ifelse(params$groupOnX,'x','y')],
         FUN=function(yy){
           if (length(yy) == 1) return(0)
-          else beeswarm::swarmx(0,yy,cex=params$cex,priority=params$priority)$x
+          else beeswarm::swarmx(
+            0,
+            yy,
+            cex=params$cex,
+            priority=params$priority,
+            #divisor is a magic number to get a reasonable baseline
+            #better option would be to figure out point size in user coords
+            xsize=ifelse(params$groupOnX,xRange,yRange)/100,
+            ysize=ifelse(params$groupOnX,yRange,xRange)/100
+          )$x
         }
       )
       return(newX+xx)

README.Rmd

@@ -92,16 +92,17 @@ Using `geom_beeswarm`:
 ggplot(iris,aes(Species, Sepal.Length)) + geom_beeswarm()
 ggplot(mpg,aes(class, hwy)) + geom_beeswarm()
 # With categorical y-axis
-ggplot(mpg,aes(hwy, class)) + geom_beeswarm()
+ggplot(mpg,aes(hwy, class)) + geom_beeswarm(cex=1.2)
 
 # ggplot doesn't pass any information about the actual device size of the points
 # to the underlying layout code, so it's important to manually adjust the `cex` 
 # parameter for best results
-ggplot(mpg,aes(class, hwy)) + geom_beeswarm(cex=5)
-ggplot(iris,aes(Species, Sepal.Length)) + geom_beeswarm(cex=4,priority='density')
+# Also watch out for points escaping from the plot with geom_beeswarm
+ggplot(mpg,aes(class, hwy)) + geom_beeswarm(cex=1.1)
+ggplot(iris,aes(Species, Sepal.Length)) + geom_beeswarm(cex=1.2,priority='density')
 
 # With automatic dodging
-ggplot(sub_mpg, aes(class, displ, color=factor(cyl))) + geom_beeswarm(dodge.width=0.7, cex=4)
+ggplot(sub_mpg, aes(class, displ, color=factor(cyl))) + geom_beeswarm(dodge.width=0.5)
 ```
 
 

README.md

@@ -142,7 +142,7 @@ ggplot(mpg,aes(class, hwy)) + geom_beeswarm()
 
 ```r
 # With categorical y-axis
-ggplot(mpg,aes(hwy, class)) + geom_beeswarm()
+ggplot(mpg,aes(hwy, class)) + geom_beeswarm(cex=1.2)
 ```
 
 <img src="README_files/figure-html/ggplot2-beeswarm-3.png" title="plot of chunk ggplot2-beeswarm" alt="plot of chunk ggplot2-beeswarm" width="432" />
@@ -151,20 +151,21 @@ ggplot(mpg,aes(hwy, class)) + geom_beeswarm()
 # ggplot doesn't pass any information about the actual device size of the points
 # to the underlying layout code, so it's important to manually adjust the `cex` 
 # parameter for best results
-ggplot(mpg,aes(class, hwy)) + geom_beeswarm(cex=5)
+# Also watch out for points escaping from the plot with geom_beeswarm
+ggplot(mpg,aes(class, hwy)) + geom_beeswarm(cex=1.1)
 ```
 
 <img src="README_files/figure-html/ggplot2-beeswarm-4.png" title="plot of chunk ggplot2-beeswarm" alt="plot of chunk ggplot2-beeswarm" width="432" />
 
 ```r
-ggplot(iris,aes(Species, Sepal.Length)) + geom_beeswarm(cex=4,priority='density')
+ggplot(iris,aes(Species, Sepal.Length)) + geom_beeswarm(cex=1.2,priority='density')
 ```
 
 <img src="README_files/figure-html/ggplot2-beeswarm-5.png" title="plot of chunk ggplot2-beeswarm" alt="plot of chunk ggplot2-beeswarm" width="432" />
 
 ```r
 # With automatic dodging
-ggplot(sub_mpg, aes(class, displ, color=factor(cyl))) + geom_beeswarm(dodge.width=0.7, cex=4)
+ggplot(sub_mpg, aes(class, displ, color=factor(cyl))) + geom_beeswarm(dodge.width=0.5)
 ```
 
 <img src="README_files/figure-html/ggplot2-beeswarm-6.png" title="plot of chunk ggplot2-beeswarm" alt="plot of chunk ggplot2-beeswarm" width="432" />

inst/doc/usageExamples.R

@@ -100,25 +100,29 @@ packageKeywords<-"visualization, display, one dimensional, grouped, groups, viol
 ###################################################
 ### code chunk number 14: dodgeBee (eval = FALSE)
 ###################################################
-##   ggplot(mapping=aes(labs,dat,color=labs2)) + geom_beeswarm(dodge.width=.8)
+##   ggplot(mapping=aes(labs,dat,color=labs2)) +
+##     geom_beeswarm(dodge.width=.8,cex=2)
 
 
 ###################################################
 ### code chunk number 15: showDodgeBee
 ###################################################
-  ggplot(mapping=aes(labs,dat,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(labs,dat,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 
 
 ###################################################
 ### code chunk number 16: dodgeYBee (eval = FALSE)
 ###################################################
-##   ggplot(mapping=aes(dat,labs,color=labs2)) + geom_beeswarm(dodge.width=.8)
+##   ggplot(mapping=aes(dat,labs,color=labs2)) +
+##     geom_beeswarm(dodge.width=.8,cex=2)
 
 
 ###################################################
 ### code chunk number 17: showDodgeYBee
 ###################################################
-  ggplot(mapping=aes(dat,labs,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(dat,labs,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 
 
 ###################################################
@@ -189,7 +193,7 @@ packageKeywords<-"visualization, display, one dimensional, grouped, groups, viol
 ##     ggtitle('tukey') + labs(x='') +
 ##     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
 ##   p6<-ggplot(mapping=aes(labs, dat)) +
-##     geom_beeswarm(alpha=.2,cex=8,size=.75) +
+##     geom_beeswarm(alpha=.2,size=.75) +
 ##     ggtitle('geom_beeswarm') + labs(x='') +
 ##     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
 ##   grid.arrange(p1, p2, p3, p4, p5, p6, ncol=3)
@@ -229,7 +233,7 @@ packageKeywords<-"visualization, display, one dimensional, grouped, groups, viol
     ggtitle('tukey') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   p6<-ggplot(mapping=aes(labs, dat)) +
-    geom_beeswarm(alpha=.2,cex=8,size=.75) +
+    geom_beeswarm(alpha=.2,size=.75) +
     ggtitle('geom_beeswarm') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   grid.arrange(p1, p2, p3, p4, p5, p6, ncol=3)

inst/doc/usageExamples.Rnw

@@ -102,15 +102,17 @@ Or on the y-axis:
 
 And with \code{geom_beeswarm}:
 <<dodgeBee, echo=TRUE, eval=FALSE>>= labs2<-factor(rep(1:2,each=n))
-  ggplot(mapping=aes(labs,dat,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(labs,dat,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 @
 \begin{center}
 <<showDodgeBee, fig=TRUE, height=3.5, width=5, echo=FALSE>>=
 <<dodgeBee>>
 @
 \end{center}
 <<dodgeYBee, echo=TRUE, eval=FALSE>>=
-  ggplot(mapping=aes(dat,labs,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(dat,labs,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 @
 \begin{center}
 <<showDodgeYBee, fig=TRUE, height=3.5, width=5, echo=FALSE>>=
@@ -189,7 +191,7 @@ The first four options are included within \code{geom_quasirandom} using the \co
     ggtitle('tukey') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   p6<-ggplot(mapping=aes(labs, dat)) +
-    geom_beeswarm(alpha=.2,cex=8,size=.75) +
+    geom_beeswarm(alpha=.2,size=.75) +
     ggtitle('geom_beeswarm') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   grid.arrange(p1, p2, p3, p4, p5, p6, ncol=3)

vignettes/usageExamples.Rnw

@@ -102,15 +102,17 @@ Or on the y-axis:
 
 And with \code{geom_beeswarm}:
 <<dodgeBee, echo=TRUE, eval=FALSE>>= labs2<-factor(rep(1:2,each=n))
-  ggplot(mapping=aes(labs,dat,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(labs,dat,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 @
 \begin{center}
 <<showDodgeBee, fig=TRUE, height=3.5, width=5, echo=FALSE>>=
 <<dodgeBee>>
 @
 \end{center}
 <<dodgeYBee, echo=TRUE, eval=FALSE>>=
-  ggplot(mapping=aes(dat,labs,color=labs2)) + geom_beeswarm(dodge.width=.8)
+  ggplot(mapping=aes(dat,labs,color=labs2)) +
+    geom_beeswarm(dodge.width=.8,cex=2)
 @
 \begin{center}
 <<showDodgeYBee, fig=TRUE, height=3.5, width=5, echo=FALSE>>=
@@ -189,7 +191,7 @@ The first four options are included within \code{geom_quasirandom} using the \co
     ggtitle('tukey') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   p6<-ggplot(mapping=aes(labs, dat)) +
-    geom_beeswarm(alpha=.2,cex=8,size=.75) +
+    geom_beeswarm(alpha=.2,size=.75) +
     ggtitle('geom_beeswarm') + labs(x='') +
     theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
   grid.arrange(p1, p2, p3, p4, p5, p6, ncol=3)