CHANGES IN VERSION 1.2.2 ------------------------ o add support of ape bootstrap analysis <2015-10-26, Mon> see https://github.com/GuangchuangYu/ggtree/issues/20 o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon> see https://github.com/GuangchuangYu/ggtree/issues/21 CHANGES IN VERSION 1.1.20 ------------------------ o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu> o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri> o bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu> o update vignette by adding r8s example <2015-09-02, Wed> o defined r8s class, see http://loco.biosci.arizona.edu/r8s/ <2015-09-02, Wed> + add r8s sample files + read.r8s, parser function + fortify method + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed> o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue> o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue> - remove 'time_scale' parameter. o defined 'raxml' class for RAxML bootstrapping analysis result <2015-09-01, Tue> + see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html + read.raxml, parser function + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods + fortify.raxml method o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue> CHANGES IN VERSION 1.1.19 ------------------------ o use fortify instead of fortify.phylo in fortify.multiPhylo, so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon> o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon> o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon> + these two packages is not commonly used, and will be loaded automatically when needed. CHANGES IN VERSION 1.1.18 ------------------------ o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none') 'unroot' is not changed. <2015-08-28. Fri> o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri> see https://github.com/hadley/ggplot2/issues/1295 o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri> o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri> CHANGES IN VERSION 1.1.17 ------------------------ o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu> o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu> o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu> o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu> o theme_transparent to make background transparent <2015-08-27, Thu> o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu> CHANGES IN VERSION 1.1.16 ------------------------ o update citation <2015-08-17, Mon> CHANGES IN VERSION 1.1.15 ------------------------ o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu> o support changing size of add_legend <2015-08-13, Thu> o reroot methods for phylo and beast <2015-08-07, Fri> CHANGES IN VERSION 1.1.14 ------------------------ o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri> CHANGES IN VERSION 1.1.13 ------------------------ o implement annotation_image <2015-08-01, Sat> o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat> o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat> CHANGES IN VERSION 1.1.12 ------------------------ o update vignette according to the changes <2015-07-31, Fri> o add mapping parameter in ggtree function <2015-07-31, Fri> o extend groupClade to support operating on tree view <2015-07-31, Fri> o extend groupOTU to support operating on tree view <2015-07-31, Fri> o new implementation of groupClade & groupOTU <2015-07-31, Fri> CHANGES IN VERSION 1.1.11 ------------------------ o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu> o better add_legend implementation. <2015-07-30, Thu> o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu> o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu> CHANGES IN VERSION 1.1.10 ------------------------ o solve overlapping branches for layout = "fan" || "radial", that are coord_polar-ized layouts. see https://github.com/GuangchuangYu/ggtree/issues/6, contributed by Vincent Bonhomme. <2015-07-22, Wed> CHANGES IN VERSION 1.1.9 ------------------------ o update add_legend to align legend text <2015-07-06, Mon> o bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed> o rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed> o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue> o add example of flip function in vignette <2015-06-30, Tue> o flip function for exchanging positions of two selected branches <2015-06-30, Tue> CHANGES IN VERSION 1.1.8 ------------------------ o update get.placement <2015-06-05, Fri> o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu> o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue> o add mask function <2015-06-02, Tue> CHANGES IN VERSION 1.1.7 ------------------------ o add example of msaplot in vignette <2015-05-22, Fri> o msaplot for adding multiple sequence alignment <2015-05-22, Fri> CHANGES IN VERSION 1.1.6 ------------------------ o add vertical_only parameter to scaleClade and set to TRUE by default. only vertical will be scaled by default. <2015-05-22, Fri> o update add_colorbar & add_legend <2015-05-21, Thu> o add example of add_legend and gheatmap in vignette <2015-05-18, Mon> o gheatmap implementation of gplot <2015-05-18, Mon> o add_legend for adding evolution distance legend <2015-05-18, Mon> CHANGES IN VERSION 1.1.5 ------------------------ o implement scaleClade <2015-05-12, Tue> CHANGES IN VERSION 1.1.4 ------------------------ o better performance of parsing beast tree <2015-05-11, Mon> + support beast tree begin with 'tree tree_1 = ' and other forms. + support file that only contains one evidence for some of the nodes/tips o update add_colorbar to auto determine the position <2015-05-04, Mon> o add_colorbar function <2015-04-30, Thu> CHANGES IN VERSION 1.1.3 ------------------------ o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu> o remove slash line in heatmap legend <2015-04-30, Thu> o update vignette to add example of merge_tree <2015-04-29, Wed> CHANGES IN VERSION 1.1.2 ------------------------ o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed> o add examples folder in inst that contains sample data <2015-04-29, Wed> o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue> o add line break if substitution longer than 50 character <2015-04-28, Tue> o support calculating branch for time scale tree <2015-04-28, Tue> o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue> o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue> o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue> o extend fortify methods to support additional fields <2015-04-28, Tue> o extend get.fields methods to support additional fields <2015-04-28, Tue> o extend tree class to support additional info by merging two tree <2015-04-28, Tue> o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue> CHANGES IN VERSION 1.1.1 ------------------------ o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon> o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon> o add Tommy in author <2015-04-27, Mon> CHANGES IN VERSION 0.99.28 ------------------------ o update vignette with floating table of content <2015-04-08, Wed> CHANGES IN VERSION 0.99.27 ------------------------ o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue> CHANGES IN VERSION 0.99.26 ------------------------ o update geom_tiplab <2015-03-31, Tue> o update plot method of beast <2015-03-17, Tue> CHANGES IN VERSION 0.99.25 ------------------------ o implement groupClade <2015-03-13, Fri> CHANGES IN VERSION 0.99.24 ------------------------ o use "round" segment end, look very better <2015-03-12, Thu> o update vignett <2015-03-11, Wed> CHANGES IN VERSION 0.99.23 ------------------------ o mv geom_hilight to hilight <2015-03-11, Wed> o mv geom_phylopic to phylopic <2015-03-11, Wed> o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed> CHANGES IN VERSION 0.99.22 ------------------------ o remove quote in beast tip/node labels <2015-03-10, Tue> CHANGES IN VERSION 0.99.21 ------------------------ o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue> CHANGES IN VERSION 0.99.19 ------------------------ o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu> CHANGES IN VERSION 0.99.18 ------------------------ o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu> CHANGES IN VERSION 0.99.17 ------------------------ o add angle and branch.y variable in cladogram layout <2015-02-10, Tue> CHANGES IN VERSION 0.99.16 ------------------------ o correct typo in vignette <2015-02-10, Tue> CHANGES IN VERSION 0.99.15 ------------------------ o fully support of replace operator, %<% <2015-02-09, Mon> CHANGES IN VERSION 0.99.14 ------------------------ o add example in groupOTU for adding legend manually <2015-02-09, Mon>. CHANGES IN VERSION 0.99.13 ------------------------ o two dimensional tree <2015-02-06, Fri> CHANGES IN VERSION 0.99.12 ------------------------ o update vignette <2015-02-04, Wed> o gzoom methods that supports all tree objects <2015-02-04, Wed> o geom_hilight layer for highlighting clade <2015-02-04, Wed> CHANGES IN VERSION 0.99.11 ------------------------ o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed> o revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed> CHANGES IN VERSION 0.99.10 ------------------------ o support y scale by category variable <2015-02-03, Tue> o support order nodes by yscale <2015-02-03, Tue> CHANGES IN VERSION 0.99.9 ------------------------ o update vignette <2015-02-02, Mon> CHANGES IN VERSION 0.99.8 ------------------------ o add get.phylopic function to read the online phylo pic and convert it to grob object, which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri> CHANGES IN VERSION 0.99.7 ------------------------ o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu> CHANGES IN VERSION 0.99.6 ------------------------ o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon> o now read.beast supports characters in support values <2015-01-18, Sun> o add example of gzoom and groupOTU in vignette <2015-01-14, Wed> o implement groupOTU methods <2015-01-14, Wed> o export get.offspring.tip <2015-01-14, Wed> CHANGES IN VERSION 0.99.5 ------------------------ o move ape and ggplot2 from Depends to Imports <2015-01-12, Mon> o get.tipseq method for paml_rst and codeml object <2015-01-08, Thu> o add gzoom function, similar to zoom function in ape <2015-01-07, Wed> o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue> o remove <<- and update vignette <2015-01-06, Tue> o update vignette and use BibTex and CSL for references <2015-01-05, Mon> o update cladogram layout <2015-01-05, Mon> o read.baseml function and update vignette with baseml example <2015-01-04, Sun> o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun> o merge all vignettes to ggtree vignette <2015-01-04, Sun> CHANGES IN VERSION 0.99.4 ------------------------ o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat> o get.subs method for hyphy object <2015-01-03, Sat> o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri> o export read.hyphy <2015-01-02, Fri> o export hyphy class <2015-01-01, Thu> o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed> o show, get.fields, get.subs and plot methods for codeml class <2014-12-30, Tue> o plot method for paml_rst class <2014-12-30, Tue> o get.subs, method for paml_rst class <2014-12-30, Tue> o show, plot, get.tree and fority methods for codeml_mlc class <2014-12-29, Mon> o codeml class <2014-12-29, Mon> o hyphy class and read.hyphy prototype <2014-12-27, Sat> o update man file and add example file of beast output <2014-12-26, Fri> o get.tree and get.fileds methods of beast class <2014-12-26, Fri> o read.beast <2014-12-26, Fri> o beast class and show method <2014-12-26, Fri> o coplot prototype<2014-12-24, Wed> o parse translation matrix in beast nexus <2014-12-24, Wed> o extract beast stats info <2014-12-23, Tue> CHANGES IN VERSION 0.99.3 ------------------------ o gplot function that can view a tree and an associated matrix simultaneously <2014-12-22, Mon> o modified vignette to show based on branch position and break the evolution distance scale <2014-12-22, Mon> o label and annotation can be put based on branch. <2014-12-22, Mon> o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun> o support unrooted layout in ggplot. <2014-12-21, Sun> o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun> CHANGES IN VERSION 0.99.2 ------------------------ o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34 of 'Inferring Phylogenies' (page 578-580) <2014-12-20, Sat> o add layout parameter in ggtree and geom_tree, now supports phylogram and cladogram <2014-12-20, Sat> o %<+% function for inserting annotation data to a tree view <2014-12-20, Sat> o update ggtree-treeAnnotation vignette <2014-12-20, Sat> CHANGES IN VERSION 0.99.1 ------------------------ o %<% function for updating tree view with a new tree <2014-12-19, Fri> o add examples in man files <2014-12-19, Fri> CHANGES IN VERSION 0.2.3 ------------------------ o add README.md <2014-12-19, Fri> o update ggtree-treeViewer vignette <2014-12-19, Fri> o use BiocStyle in vignette <2014-12-19, Fri> o geom_nplace and geom_place layer <2014-12-18, Thu> o add theme_tree2 theme for showing evolution distance <2014-12-18, Thu> o rm.singleton.newick now supports internal node like: ((()X, ()Y)Z)AA, in which Z is a singleton. <2014-12-15, Mon> CHANGES IN VERSION 0.2.2 ------------------------ o rm.singleton.newick <2014-12-09, Tue> o as.binary method <2014-12-09, Tue> CHANGES IN VERSION 0.2.1 ------------------------ o geom_eplace <2014-12-07, Sun> CHANGES IN VERSION 0.2.0 ------------------------ o read.jplace to read the jplace file <2014-12-05, Fri> o jplace class for storing information of jplace file <2014-12-05, Fri> o show method of jplace class <2014-12-05, Fri> o get.tree method to get tree from jplace class <2014-12-05, Fri> o extend ggplot2 to support jplace class <2014-12-05, Fri> CHANGES IN VERSION 0.1.1 ------------------------ o add distance legend in ggtree <2014-12-05, Fri> CHANGES IN VERSION 0.1.0 ------------------------ o support ladderize tree <2014-12-05, Fri> o implement geom_tree, geom_tiplab, geom_tippoint, geom_aline and theme_tree <2014-12-04, Thu> o extend ggplot to support phylo object and implement ggtree function <2014-12-04, Thu> o implement fortify function <2014-12-04, Thu> o add getRoot, isRoot and getParent functions <2014-12-03, Wed>