CHANGES IN VERSION 1.3.14
------------------------
o update theme_tree2 due to the issue of https://github.com/hadley/ggplot2/issues/1567 <2016-03-05, Sat>
o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
+ see https://github.com/GuangchuangYu/ggtree/issues/46
o subview and inset now supports annotating with img files <2016-02-23, Tue>
CHANGES IN VERSION 1.3.13
------------------------
o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
o geom_cladelabel work with collapse <2016-02-07, Sun>
+ see https://github.com/GuangchuangYu/ggtree/issues/38
CHANGES IN VERSION 1.3.12
------------------------
o exchange function name of geom_tree and geom_tree2 <2016-01-25, Mon>
o solved issues of geom_tree2 <2016-01-25, Mon>
+ https://github.com/hadley/ggplot2/issues/1512
o colnames_level parameter in gheatmap <2016-01-25, Mon>
o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
CHANGES IN VERSION 1.3.11
------------------------
o solved issues of geom_tree2 <2016-01-25, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/36
o change compute_group() to compute_panel in geom_tree2() <2016-01-21, Thu>
+ fixed issue, https://github.com/GuangchuangYu/ggtree/issues/36
o support phyloseq object <2016-01-21, Thu>
o update geom_point2, geom_text2 and geom_segment2 to support setup_tree_data <2016-01-21, Thu>
o implement geom_tree2 layer that support duplicated node records via the setup_tree_data function <2016-01-21, Thu>
o rescale_tree function for rescaling branch length of tree object <2016-01-20, Wed>
o upgrade set_branch_length, now branch can be rescaled using feature in extraInfo slot <2016-01-20, Wed>
CHANGES IN VERSION 1.3.10
------------------------
o remove dependency of gridExtra by implementing multiplot function instead of using grid.arrange <2016-01-20, Wed>
o remove dependency of colorspace <2016-01-20, Wed>
o support phylip tree format and update vignette of phylip example <2016-01-15, Fri>
CHANGES IN VERSION 1.3.9
------------------------
o optimize getYcoord <2016-01-14, Thu>
o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>
o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.
these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>
+ > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.
CHANGES IN VERSION 1.3.8
------------------------
o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
o add viewClade function <2016-01-12, Tue>
o support obkData object defined by OutbreakTools <2016-01-12, Tue>
o update vignettes <2016-01-07, Thu>
o 05 advance tree annotation vignette <2016-01-04, Mon>
o export theme_inset <2016-01-04, Mon>
o inset, nodebar, nodepie functions <2015-12-31, Thu>
CHANGES IN VERSION 1.3.7
------------------------
o split the long vignette to several vignettes
+ 00 ggtree <2015-12-29, Tue>
+ 01 tree data import <2015-12-28, Mon>
+ 02 tree visualization <2015-12-28, Mon>
+ 03 tree manipulation <2015-12-28, Mon>
+ 04 tree annotation <2015-12-29, Tue>
CHANGES IN VERSION 1.3.6
------------------------
o MRCA function for finding Most Recent Common Ancestor among a vector of tips <2015-12-22, Tue>
o geom_cladelabel: add bar and label to annotate a clade <2015-12-21, Mon>
- remove annotation_clade and annotation_clade2 functions.
o geom_treescale: tree scale layer. (add_legend was removed) <2015-12-21, Mon>
CHANGES IN VERSION 1.3.5
------------------------
o bug fixed, read.nhx now works with scientific notation <2015-11-30, Mon>
+ see https://github.com/GuangchuangYu/ggtree/issues/30
CHANGES IN VERSION 1.3.4
------------------------
o rename beast feature when name conflict with reserve keywords (label, branch, etc) <2015-11-27, Fri>
o get_clade_position function <2015-11-26, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/28
o get_heatmap_column_position function <2015-11-25, Wed>
+ see https://github.com/GuangchuangYu/ggtree/issues/26
o support NHX (New Hampshire X) format via read.nhx function <2015-11-17, Tue>
o bug fixed in extract.treeinfo.jplace <2015-11-17, Thu>
CHANGES IN VERSION 1.3.3
------------------------
o support color=NULL in gheatmap, then no colored line will draw within the heatmap <2015-10-30, Fri>
o add `angle` for also rectangular, so that it will be available for layout='rectangular' following by coord_polar() <2015-10-27, Tue>
CHANGES IN VERSION 1.3.2
------------------------
o update vignette, add example of ape bootstrap and phangorn ancestral sequences <2015-10-26, Mon>
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 1.3.1
------------------------
o change angle to angle + 90, so that label will in radial direction <2015-10-22, Thu>
+ see https://github.com/GuangchuangYu/ggtree/issues/17
o na.rm should be always passed to layer(), fixed it in geom_hilight and geom_text2 <2015-10-21, Wed>
+ see https://github.com/hadley/ggplot2/issues/1380
o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>
CHANGES IN VERSION 1.3.0
------------------------
o BioC 3.3 branch
CHANGES IN VERSION 1.1.21
------------------------
o support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>
o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
CHANGES IN VERSION 1.1.20
------------------------
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>
