NEWS
da0f0f7f
 CHANGES IN VERSION 1.5.16
 ------------------------
  o fixed R check <2016-10-10, Mon>
    + check.aes parameter is not available in release version of ggplot2 yet
  
bedefde1
 CHANGES IN VERSION 1.5.15
 ------------------------
  o check.aes for layers defined in ggtree <2016-10-07, Fri>
  o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
    + https://github.com/GuangchuangYu/ggtree/issues/78
 
e44561c1
 CHANGES IN VERSION 1.5.14
 ------------------------
97e7d34f
  o subset tip in geom_tiplab2 <2016-10-05, Wed>
102483c0
  o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
    + https://github.com/hadley/ggplot2/issues/1797
deef5815
  o unit test for groupOTU and groupClade <2016-09-22, Thu>
  o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
e44561c1
  o update angle calculation for geom_tiplab <2016-09-13, Thu>
  o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). <2016-09-13, Tue>
    + currently only phylo object supported.
    + add test for as.polytomy
deef5815
 
1652e9e8
 CHANGES IN VERSION 1.5.13
 ------------------------
  o facet_plot for plotting data with tree <2016-09-06, Tue>
  o more parameters for column names in gheatmap <2016-09-06, Tue>
    + colnames_angle
    + colnames_offset_x
    + colnames_offset_y
    + hjust
  o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
deef5815
 
6478c43c
 CHANGES IN VERSION 1.5.12
 ------------------------
1652e9e8
  o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
6478c43c
  o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
deef5815
 
d3869c64
 CHANGES IN VERSION 1.5.11
 ------------------------
d398a2b0
  o gheatmap works with matrix <2016-08-28, Sun>
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ
  o support parsing expression in geom_strip <2016-08-18, Thu>
d3869c64
  o bug fixed in geom_tiplab <2016-08-17, Wed>
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
  o update citation info, add doi. <2016-08-16, Tue>
deef5815
 
a2690c83
 CHANGES IN VERSION 1.5.10
 ------------------------
  o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
    + https://github.com/GuangchuangYu/ggtree/issues/72
deef5815
 
92812ded
 CHANGES IN VERSION 1.5.9
 ------------------------
  o update citation info <2016-08-12, Fri>
deef5815
 
c1e35f48
 CHANGES IN VERSION 1.5.8
 ------------------------
  o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
  o geom_cladelabel support parsing expression <2016-08-11, Thu>
deef5815
 
ef017f6c
 CHANGES IN VERSION 1.5.7
 ------------------------
19219dd5
  o geom_strip can accept taxa name as input but labeling strip will not supported.
    To support labeling strip, user need to input node id  <2016-07-27, Wed>
deef5815
  o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
 
5bb1376e
 CHANGES IN VERSION 1.5.6
 ------------------------
a90eeffd
  o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
    + still needed for building vignette and for processing FASTA file
  o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>
    + the package is still needed if user want to annotate tree with image file
  o `%<+%` now works with tbl_df <2016-07-21, Thu>
    + https://github.com/GuangchuangYu/ggtree/issues/66
dbaa7fd2
  o identify method for ggtree <2016-06-28, Tue>
    + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
5bb1376e
  o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
    + see https://github.com/GuangchuangYu/ggtree/pull/64
 
85777d7b
 CHANGES IN VERSION 1.5.5
 ------------------------
5e6f5a80
  o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
b1e524c4
  o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
85777d7b
  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
    + as.Date won't work for BCE time.
    + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
deef5815
 
55bbcddb
 CHANGES IN VERSION 1.5.4
 ------------------------
85777d7b
  o reroot method for raxml object <2016-05-22, Sun>
e69e5f4f
  o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
69b0d0e9
  o bug fixed in collapse <2016-05-20, Fri>
    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
ded558eb
  o use byte compiler <2016-05-18, Wed>
deef5815
  o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
55bbcddb
  o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
 
3e0a61f1
 CHANGES IN VERSION 1.5.3
 ------------------------
10f32b5b
  o add examples in vignettes <2016-05-13, Fri>
    + add fan layout example in treeVisualization vignette
    + add open_tree and rotate_tree example in treeManipulation vignette
cf039511
  o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
deef5815
  o rotate_tree and open_tree function <2016-05-12, Thu>
3e0a61f1
  o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
deef5815
  o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
55bbcddb
 
266b20f1
 CHANGES IN VERSION 1.5.2
 ------------------------
98e51b96
  o add multiplot in ggtreeUtilities vignette <2016-05-12, Thu>
892bdd32
  o add example of integrate user's data using phylo4d in treeAnnotation vignette <2016-05-11, Wed>
1949a7f4
  o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>
  o geom_hilight now supports hilight tips <2016-05-10, Tue>
    + https://github.com/GuangchuangYu/ggtree/issues/53
fedfaec9
  o more accurate ylim & angle for circular layout <2016-05-10, Tue>
    + https://github.com/GuangchuangYu/ggtree/issues/40
266b20f1
  o supports phylo4d object <2016-05-10, Tue>
    + https://github.com/GuangchuangYu/ggtree/issues/47
deef5815
 
3ba777c5
 CHANGES IN VERSION 1.5.1
 ------------------------
  o update vignettes <2016-05-10, Tue>
    + add geom_range example in treeImport
    + add geom_strip and geom_taxalink example in treeAnnotation
    + add ggtreeUtilities vignette
  o gheatmap now works with data.frame of only one column <2016-05-09, Mon>
    + contributed by Justin Silverman <jsilve24@gmail.com>
    + https://github.com/GuangchuangYu/ggtree/pull/57
  o geom_strip for associated taxa <2016-05-09, Mon>
    + https://github.com/GuangchuangYu/ggtree/issues/52
deef5815
 
3ba777c5
 CHANGES IN VERSION 1.4.0
 ------------------------
  o BioC 3.3 released <2016-05-05, Thu>
deef5815
 
9cfed15f
 CHANGES IN VERSION 1.3.16
 ------------------------
8a5c744d
  o geom_treescale() supports family argument <2016-04-27, Wed>
    + https://github.com/GuangchuangYu/ggtree/issues/56
9cfed15f
  o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu>
    + https://github.com/GuangchuangYu/ggtree/issues/54
f2aa6adb
  o support passing textConnection(text_string) as a file <2016-04-21, Thu>
1207e25e
    + contributed by Casey Dunn <casey_dunn@brown.edu>
f2aa6adb
    + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693
deef5815
 
0bd36b2a
 CHANGES IN VERSION 1.3.15
 ------------------------
bf3a8df9
  o geom_tiplab2 supports parameter hjust <2016-04-18, Mon>
7d9641c6
  o geom_tiplab and geom_tiplab2 support using geom_label2 by passing geom="label" <2016-04-07, Thu>
  o geom_label2 that support subsetting <2016-04-07, Thu>
ee6dfb2c
  o geom_tiplab2 for adding tip label of circular layout <2016-04-06, Wed>
d8db8bda
  o use plot$plot_env to access ggplot2 parameter <2016-04-06, Wed>
deef5815
  o geom_taxalink for connecting related taxa <2016-04-01, Fri>
0bd36b2a
  o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>
deef5815
 
37f7a26a
 CHANGES IN VERSION 1.3.14
 ------------------------
0cf0c570
  o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>
2a711f87
  o update theme_tree2 due to the issue of https://github.com/hadley/ggplot2/issues/1567 <2016-03-05, Sat>
5d4e7548
  o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
    + see https://github.com/GuangchuangYu/ggtree/issues/46
37f7a26a
  o subview and inset now supports annotating with img files <2016-02-23, Tue>
deef5815
 
e4ea056a
 CHANGES IN VERSION 1.3.13
 ------------------------
  o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
0cf0c570
  o geom_cladelabel works with collapse <2016-02-07, Sun>
deef5815
    + see https://github.com/GuangchuangYu/ggtree/issues/38
e4ea056a
 
 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>
deef5815
  o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
 
e4ea056a
 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>
deef5815
 
df059d88
 CHANGES IN VERSION 1.3.10
 ------------------------
e4ea056a
  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>
df059d88
  o support phylip tree format and update vignette of phylip example <2016-01-15, Fri>
 
0b5c08bd
 CHANGES IN VERSION 1.3.9
 ------------------------
df059d88
  o optimize getYcoord <2016-01-14, Thu>
a1cac40c
  o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>
0b5c08bd
  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.
deef5815
 
d5c2a530
 CHANGES IN VERSION 1.3.8
 ------------------------
0b5c08bd
  o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
869c8fbc
  o add viewClade function <2016-01-12, Tue>
  o support obkData object defined by OutbreakTools <2016-01-12, Tue>
16dd3ab8
  o update vignettes <2016-01-07, Thu>
d5c2a530
  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>
deef5815
 
af18d052
 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>
0b5c08bd
    + 03 tree manipulation <2015-12-28, Mon>
af18d052
    + 04 tree annotation <2015-12-29, Tue>
deef5815
 
6c9cd355
 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>
deef5815
 
6c9cd355
 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>
deef5815
 
6c9cd355
 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>
deef5815
 
6c9cd355
 CHANGES IN VERSION 1.3.2
0003d656
 ------------------------
6c9cd355
  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
deef5815
 
6c9cd355
 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>
deef5815
 
0bd36b2a
 CHANGES IN VERSION 1.2.0
6c9cd355
 ------------------------
0bd36b2a
  o BioC 3.2 released
deef5815
 
6c9cd355
 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>
0003d656
  o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
6c9cd355
  o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
deef5815
 
6c9cd355
 CHANGES IN VERSION 1.1.20
 ------------------------
0003d656
  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
deef5815
  o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
0003d656
  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>
deef5815
 
0003d656
 CHANGES IN VERSION 1.1.19
 ------------------------
deef5815
  o use fortify instead of fortify.phylo in fortify.multiPhylo,
0003d656
    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.
deef5815
 
1d4d6914
 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>
deef5815
  o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
 
2ab2876d
 CHANGES IN VERSION 1.1.17
 ------------------------
7182a17d
  o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
64359009
  o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
2ab2876d
  o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
deef5815
  o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
2ab2876d
  o theme_transparent to make background transparent <2015-08-27, Thu>
deef5815
  o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
 
8d0a47fb
 CHANGES IN VERSION 1.1.16
 ------------------------
  o update citation <2015-08-17, Mon>
deef5815
 
6e4f67da
 CHANGES IN VERSION 1.1.15
 ------------------------
b73d586d
  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>
6e4f67da
  o reroot methods for phylo and beast <2015-08-07, Fri>
deef5815
 
b8403a57
 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>
deef5815
 
68c7ac99
 CHANGES IN VERSION 1.1.13
 ------------------------
5cfb0ffa
  o implement annotation_image <2015-08-01, Sat>
68c7ac99
  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>
deef5815
 
94bf49f9
 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>
deef5815
 
94bf49f9
 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>
deef5815
 
d581c706
 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>
 
61678cbb
 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>
deef5815
 
2dc67dc5
 CHANGES IN VERSION 1.1.8
 ------------------------
dc590c34
  o update get.placement <2015-06-05, Fri>
2dcb9db3
  o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
2dc67dc5
  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>
deef5815
 
54a49cea
 CHANGES IN VERSION 1.1.7
 ------------------------
1e6d2bbb
  o add example of msaplot in vignette <2015-05-22, Fri>
54a49cea
  o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
deef5815
 
ad07ec89
 CHANGES IN VERSION 1.1.6
 ------------------------
8d5be3f5
  o add vertical_only parameter to scaleClade and set to TRUE by default.
    only vertical will be scaled by default. <2015-05-22, Fri>
c0c066a5
  o update add_colorbar & add_legend <2015-05-21, Thu>
deef5815
  o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
ad07ec89
  o gheatmap implementation of gplot <2015-05-18, Mon>
  o add_legend for adding evolution distance legend <2015-05-18, Mon>
deef5815
 
afa023c5
 CHANGES IN VERSION 1.1.5
 ------------------------
  o implement scaleClade <2015-05-12, Tue>
deef5815
 
85f33ddc
 CHANGES IN VERSION 1.1.4
 ------------------------
03beafbf
  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
f7acd3a2
  o update add_colorbar to auto determine the position <2015-05-04, Mon>
85f33ddc
  o add_colorbar function <2015-04-30, Thu>
deef5815
 
a61d05b4
 CHANGES IN VERSION 1.1.3
63bdf4e0
 ------------------------
85f33ddc
  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>
63bdf4e0
  o update vignette to add example of merge_tree <2015-04-29, Wed>
deef5815
 
a61d05b4
 CHANGES IN VERSION 1.1.2
 ------------------------
63bdf4e0
  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>
0003d656
  o support calculating branch for time scale tree <2015-04-28, Tue>
63bdf4e0
  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>
deef5815
 
b893400f
 CHANGES IN VERSION 1.1.1
 ------------------------
ffdebeea
  o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
f672c8b8
  o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
b893400f
  o add Tommy in author <2015-04-27, Mon>
deef5815
 
a84e6bef
 CHANGES IN VERSION 0.99.28
 ------------------------
  o update vignette with floating table of content <2015-04-08, Wed>
deef5815
 
16462216
 CHANGES IN VERSION 0.99.27
 ------------------------
  o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>
 
a8a929b2
 CHANGES IN VERSION 0.99.26
 ------------------------
ca45db4f
  o update geom_tiplab <2015-03-31, Tue>
a8a929b2
  o update plot method of beast <2015-03-17, Tue>
deef5815
 
db1e112f
 CHANGES IN VERSION 0.99.25
 ------------------------
  o implement groupClade <2015-03-13, Fri>
deef5815
 
dd6f7cc4
 CHANGES IN VERSION 0.99.24
 ------------------------
2ed134e4
  o use "round" segment end, look very better <2015-03-12, Thu>
dd6f7cc4
  o update vignett <2015-03-11, Wed>
deef5815
 
2245dbf2
 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>
deef5815
  o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
 
41edd910
 CHANGES IN VERSION 0.99.22
 ------------------------
  o remove quote in beast tip/node labels <2015-03-10, Tue>
deef5815
 
d319319f
 CHANGES IN VERSION 0.99.21
f93f6d08
 ------------------------
d319319f
  o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
deef5815
 
e0b5eb2f
 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>
deef5815
 
f19ae4ad
 CHANGES IN VERSION 0.99.18
 ------------------------
  o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
deef5815
 
27eb80b2
 CHANGES IN VERSION 0.99.17
 ------------------------
  o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
deef5815
 
52d58a64
 CHANGES IN VERSION 0.99.16
 ------------------------
  o correct typo in vignette <2015-02-10, Tue>
 
094f0c6d
 CHANGES IN VERSION 0.99.15
 ------------------------
  o fully support of replace operator, %<% <2015-02-09, Mon>
deef5815
 
5ec77211
 CHANGES IN VERSION 0.99.14
 ------------------------
  o add example in groupOTU for adding legend manually <2015-02-09, Mon>.
 
f461013b
 CHANGES IN VERSION 0.99.13
 ------------------------
  o two dimensional tree <2015-02-06, Fri>
deef5815
 
cb732553
 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>
deef5815
  o geom_hilight layer for highlighting clade <2015-02-04, Wed>
 
4738a3fe
 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>
 
126089a9
 CHANGES IN VERSION 0.99.10
 ------------------------
4738a3fe
  o support y scale by category variable <2015-02-03, Tue>
126089a9
  o support order nodes by yscale <2015-02-03, Tue>
 
be76b050
 CHANGES IN VERSION 0.99.9
 ------------------------
  o update vignette <2015-02-02, Mon>
deef5815
 
64092992
 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>
deef5815
 
2b076745
 CHANGES IN VERSION 0.99.7
 ------------------------
7529cf31
  o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>
2b076745
 
b921de96
 CHANGES IN VERSION 0.99.6
 ------------------------
a4ffa2e3
  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>
deef5815
  o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
b921de96
  o implement groupOTU methods <2015-01-14, Wed>
  o export get.offspring.tip <2015-01-14, Wed>
 
0c8aaf33
 CHANGES IN VERSION 0.99.5
 ------------------------
b921de96
  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>
0c8aaf33
  o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
  o remove <<- and update vignette <2015-01-06, Tue>
deef5815
  o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
0c8aaf33
  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
 ------------------------
deef5815
  o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
0c8aaf33
  o get.subs method for hyphy object <2015-01-03, Sat>
deef5815
  o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
0c8aaf33
  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>
deef5815
  o beast class and show method <2014-12-26, Fri>
0c8aaf33
  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>
deef5815
 
0c8aaf33
 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>