Browse code

geom_cladelabel

GuangchuangYu authored on 11/08/2016 06:53:22
Showing11 changed files

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@@ -1,8 +1,9 @@
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-TODO.md
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 .travis.yml
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-appveyor.yml
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 .gitignore
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 .svnignore
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-Makefile
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 ^appveyor\.yml$
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+^.*\.DS_Store
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+TODO.md
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+appveyor.yml
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+Makefile
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 README.Rmd
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@@ -1,7 +1,7 @@
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 Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.7
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+Version: 1.5.8
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
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@@ -14,6 +14,10 @@ build:
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 	cd ..;\
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 	R CMD build $(PKGSRC)
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+build2:
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+	cd ..;\
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+	R CMD build --no-build-vignettes $(PKGSRC)
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+
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 install:
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 	cd ..;\
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 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
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@@ -22,6 +26,10 @@ check: build
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 	cd ..;\
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 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
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+bioccheck:
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+	cd ..;\
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+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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+
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 clean:
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 	cd ..;\
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 	$(RM) -r $(PKGNAME).Rcheck/
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@@ -1,3 +1,8 @@
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+CHANGES IN VERSION 1.5.8
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+------------------------
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+ o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
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+ o geom_cladelabel support parsing expression <2016-08-11, Thu>
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+ 
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 CHANGES IN VERSION 1.5.7
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 ------------------------
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  o geom_strip can accept taxa name as input but labeling strip will not supported.
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@@ -12,15 +12,19 @@
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 ##' @param angle angle of text
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 ##' @param geom one of 'text' or 'label'
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 ##' @param hjust hjust
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+##' @param color color for clade & label, of length 1 or 2
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 ##' @param fill fill label background, only work with geom='label'
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 ##' @param family sans by default, can be any supported font
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+##' @param parse logical, whether parse label
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 ##' @param ... additional parameter
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 ##' @return ggplot layers
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 ##' @export
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 ##' @author Guangchuang Yu
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 geom_cladelabel <- function(node, label, offset=0, offset.text=0,
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                             align=FALSE, barsize=0.5, fontsize=3.88,
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-                            angle=0, geom="text", hjust = 0, fill=NA, family="sans", ...) {
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+                            angle=0, geom="text", hjust = 0,
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+                            color = NULL, fill=NA,
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+                            family="sans", parse=FALSE, ...) {
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     mapping <- NULL
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     data <- NULL
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     position <- "identity"
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@@ -28,30 +32,73 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0,
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     na.rm <- TRUE
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     inherit.aes <- FALSE
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-    if (geom == "text") {
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-        ## no fill parameter
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-        layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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-                                    align=align, size=fontsize, angle=angle, family=family,
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-                                    mapping=mapping, data=data, geom=geom, hjust=hjust,
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-                                    position=position, show.legend = show.legend,
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-                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)
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-        
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+    if (!is.null(color)) {
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+        if (length(color) > 2) {
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+            stop("color should be of length 1 or 2")
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+        }
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+        if (length(color) == 0) {
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+            color = NULL
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+        } else if (length(color) == 1) {
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+            barcolor <- color
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+            labelcolor <- color
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+        } else {
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+            barcolor <- color[1]
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+            labelcolor <- color[2]
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+        }
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+    }
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+
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+    if (is.null(color)) {
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+        if (geom == "text") {
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+            ## no fill parameter
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+            layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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+                                        align=align, size=fontsize, angle=angle, family=family,
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+                                        mapping=mapping, data=data, geom=geom, hjust=hjust,
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+                                        position=position, show.legend = show.legend,
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+                                        inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)
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+            
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+        } else {
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+            layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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+                                        align=align, size=fontsize, angle=angle, fill=fill,family=family,
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+                                        mapping=mapping, data=data, geom=geom, hjust=hjust,
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+                                        position=position, show.legend = show.legend,
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+                                        inherit.aes = inherit.aes, na.rm=na.rm,
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+                                        parse = parse, ...)
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+        }
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+
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+        layer_bar <- stat_cladeBar(node=node, offset=offset, align=align,
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+                                   size=barsize,
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+                                   mapping=mapping, data=data, 
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+                                   position=position, show.legend = show.legend,
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+                                   inherit.aes = inherit.aes, na.rm=na.rm, ...)
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     } else {
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-        layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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-                                    align=align, size=fontsize, angle=angle, fill=fill,family=family,
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-                                    mapping=mapping, data=data, geom=geom, hjust=hjust,
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-                                    position=position, show.legend = show.legend,
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-                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)
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+        if (geom == "text") {
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+            ## no fill parameter
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+            layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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+                                        align=align, size=fontsize, angle=angle, color=labelcolor, family=family,
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+                                        mapping=mapping, data=data, geom=geom, hjust=hjust,
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+                                        position=position, show.legend = show.legend,
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+                                        inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)
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+            
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+        } else {
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+            layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text,
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+                                        align=align, size=fontsize, angle=angle, color=labelcolor, fill=fill,family=family,
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+                                        mapping=mapping, data=data, geom=geom, hjust=hjust,
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+                                        position=position, show.legend = show.legend,
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+                                        inherit.aes = inherit.aes, na.rm=na.rm,
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+                                        parse = parse, ...)
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+        }
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+
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+        layer_bar <- stat_cladeBar(node=node, offset=offset, align=align,
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+                                   size=barsize, color = barcolor,
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+                                   mapping=mapping, data=data, 
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+                                   position=position, show.legend = show.legend,
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+                                   inherit.aes = inherit.aes, na.rm=na.rm, ...)
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+        
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     }
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     list(
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-        stat_cladeBar(node=node, offset=offset, align=align,
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-                      size=barsize,
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-                      mapping=mapping, data=data, 
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-                      position=position, show.legend = show.legend,
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-                      inherit.aes = inherit.aes, na.rm=na.rm, ...),
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-        
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-        layer_text
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+       layer_bar,
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+       layer_text
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     )
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 }
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... ...
@@ -59,7 +106,8 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0,
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 stat_cladeText <- function(mapping=NULL, data=NULL,
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                            geom="text", position="identity",
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                            node, label, offset, align, ...,
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-                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
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+                           show.legend=NA, inherit.aes=FALSE,
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+                           na.rm=FALSE, parse=FALSE) {
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     default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent)
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     if (is.null(mapping)) {
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         mapping <- default_aes
... ...
@@ -75,10 +123,11 @@ stat_cladeText <- function(mapping=NULL, data=NULL,
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           show.legend = show.legend,
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           inherit.aes = inherit.aes,
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           params=list(node=node,
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-                      label=label,
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-                      offset=offset,
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-                      align=align,
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-                      na.rm=na.rm,
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+                      label  = label,
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+                      offset = offset,
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+                      align  = align,
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+                      na.rm  = na.rm,
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+                      parse  = parse,
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                       ...)
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           )
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@@ -88,7 +137,7 @@ stat_cladeBar <- function(mapping=NULL, data=NULL,
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                           geom="segment", position="identity",
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                           node, offset, align,  ...,
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                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
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-    default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent)
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+    default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y)
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     if (is.null(mapping)) {
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         mapping <- default_aes
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     } else {
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@@ -14,7 +14,7 @@ geom_range <- function(range="height_0.95_HPD", ...) {
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     na.rm = TRUE
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     inherit.aes = FALSE    
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-    default_aes <- aes_(x=~x, y=~y)
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+    default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y)
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     mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range))
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@@ -105,7 +105,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,
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                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
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     if (is.null(label) || is.na(label)) {
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-        default_aes <- aes_(x=~x, y=~y, node=~node, label=~label)
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+        default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)
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     } else {
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         default_aes <- aes_(x=~x, y=~y, node=~node)
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     }
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@@ -18,10 +18,10 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {
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     na.rm = TRUE
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     inherit.aes = FALSE    
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-    mapping <- aes_(x=~x, y=~y, node=~node, label=~label)
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+    mapping <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)
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     layer(stat=StatTaxalink,
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-          mapping=aes_(x=~x, y=~y, node=~node, label=~label),
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+          mapping=mapping,
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           geom=GeomCurve,
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           position='identity',
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           show.legend=show.legend,
... ...
@@ -45,7 +45,7 @@ stat_treeScaleLine <- function(mapping=NULL, data=NULL,
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                            xx, yy, width, offset, color, ..., 
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                            show.legend=NA, inherit.aes=FALSE, na.rm=FALSE){
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-    default_aes <- aes_(x=~x, y=~y)
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+    default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y)
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     if (is.null(mapping)) {
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         mapping <- default_aes
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     } else {
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@@ -74,7 +74,7 @@ stat_treeScaleText <- function(mapping=NULL, data=NULL,
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                                xx, yy, width, offset, color, ...,
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                                show.legend=NA, inherit.aes=TRUE, na.rm=FALSE) {
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-    default_aes <- aes_(x=~x, y=~y)
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+    default_aes <- aes_(x=~x, y=~y, label=~label)
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     if (is.null(mapping)) {
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         mapping <- default_aes
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     } else {
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@@ -6,7 +6,7 @@
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 \usage{
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 geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE,
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   barsize = 0.5, fontsize = 3.88, angle = 0, geom = "text", hjust = 0,
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-  fill = NA, family = "sans", ...)
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+  color = NULL, fill = NA, family = "sans", parse = FALSE, ...)
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 }
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 \arguments{
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 \item{node}{selected node}
... ...
@@ -29,10 +29,14 @@ geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE,
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 \item{hjust}{hjust}
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+\item{color}{color for clade & label, of length 1 or 2}
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+
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 \item{fill}{fill label background, only work with geom='label'}
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 \item{family}{sans by default, can be any supported font}
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+\item{parse}{logical, whether parse label}
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+
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 \item{...}{additional parameter}
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 }
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 \value{
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new file mode 100644
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@@ -0,0 +1,9 @@
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+context('geom_cladelabel')
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+
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+
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+test_that('geom_cladelabel support parsing expression', {
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+    p <- ggtree(rtree(30)) + geom_cladelabel(node=40, label='paste(italic("species name"), "accession number")', parse=T)
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+    expect_true(is.ggplot(p))
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+})
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+
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+