1. ggtree
  2. Commit 1cfeeff11973e7538ec7b18c3d79ad5cbaf33026
Browse code

Updated tidytree::rotateTreePoints() to rotate labels correctly.

JustGitting authored on 07/09/2017 04:14:01
Showing 129 changed files
R/tidytree.R
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@@ -643,18 +643,26 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){
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   }
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-  # Now update labels of rotated tree.
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+  # Now update tip labels of rotated tree.
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+  # angle is in range [0, 360]
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   for(node in nodes){
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-    # Update label angle if not root node.
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-    # get parent
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-    parent_id <- getParent.df(df, node)
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-    # if 'node' is not root, then update label angle.
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-    if( parent_id != 0){
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-      theta_parent_child <- getNodeAngle.df(df, parent_id, node)
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-      if(!is.na(theta_parent_child)){
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-        # Update tip label angle, that is parallel to edge.
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-        #df[node, 'angle'] <- -90 - 180 * theta_parent_child * sign(theta_parent_child - 1)
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-        df[node, 'angle'] <- 180 * theta_parent_child
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+    # Update label angle of tipnode if not root node.
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+    if( isTip.df(df, node) ){
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+      # get parent
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+      parent_id <- getParent.df(df, node)
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+      # if 'node' is not root, then update label angle.
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+      if( parent_id != 0 ){
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+        theta_parent_child <- getNodeAngle.df(df, parent_id, node)
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+        if(!is.na(theta_parent_child)){
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+          # Update tip label angle, that is parallel to edge.
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+          #df[node, 'angle'] <- -90 - 180 * theta_parent_child * sign(theta_parent_child - 1)
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+          if(theta_parent_child > 0 ){
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+            df[node, 'angle'] <- 180 * theta_parent_child
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+          }else if(theta_parent_child < 0 ){
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+            df[node, 'angle'] <- 180 * ( theta_parent_child + 2 )
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+          }
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+
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+        }
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       }
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     }
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   }
ggtree/CITATION
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+citHeader("To cite ggtree in publications use:")
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+
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+citEntry(
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+    entry  = "article",
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+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
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+    author = personList(
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+        as.person("Guangchuang Yu"),
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+        as.person("David Smith"),
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+        as.person("Huachen Zhu"),
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+        as.person("Yi Guan"),
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+        as.person("Tommy Tsan-Yuk Lam")
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+        ),
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+    year    = "2017",
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+    journal = "Methods in Ecology and Evolution",
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+    volume  = "8",
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+    issue   = "1",
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+    number  = "",
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+    pages   = "28-36",
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+    doi     = "10.1111/2041-210X.12628",
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+    PMID    = "",
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+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract",
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+    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
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+        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
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+        "Methods in Ecology and Evolution 2017, 8(1):28-36")
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+)
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+
ggtree/DESCRIPTION
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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
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+        trees with their covariates and other associated data
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+Version: 1.9.1
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+Authors@R: c(
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+	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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+	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
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+	   person("Justin", "Silverman", email = "jsilve24@gmail.com", rol = "ctb")
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+	   )
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+Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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+Description: 'ggtree' extends the 'ggplot2' plotting system which implemented
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+    the grammar of graphics. 'ggtree' is designed for visualization and annotation
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+    of phylogenetic trees with their covariates and other associated data.
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+Depends: R (>= 3.3.2), ggplot2 (>= 2.2.0), treeio
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+Imports: ape, grDevices, grid, magrittr, methods, rvcheck, tidyr, utils
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+Suggests: Biostrings, colorspace, EBImage, emojifont, knitr, prettydoc,
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+        rmarkdown, scales, testthat
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+VignetteBuilder: knitr
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+ByteCompile: true
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+License: Artistic-2.0
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+URL: https://guangchuangyu.github.io/ggtree
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+BugReports: https://github.com/GuangchuangYu/ggtree/issues
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+Packaged: 2014-12-03 08:16:14 UTC; root
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+biocViews: Alignment, Annotation, Clustering, DataImport,
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+        MultipleSequenceAlignment, ReproducibleResearch, Software,
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+        Visualization
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+RoxygenNote: 6.0.1
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+Author: Guangchuang Yu [aut, cre, cph],
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+  Tommy Tsan-Yuk Lam [aut, ths],
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+  Justin Silverman [ctb]
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+Built: R 3.3.2; ; 2017-07-07 06:08:46 UTC; windows
ggtree/INDEX
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+%+>%                    %+>%
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+%<%                     %<%
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+%<+%                    %<+%
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+%>%                     pipe
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+.                       .
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+Date2decimal            Date2decimal
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+MRCA                    MRCA
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+NJ                      NJ
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+StatBalance             StatBalance
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+add_colorbar            add_colorbar
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+annotation_image        annotation_image
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+apeBoot                 apeBoot
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+applyLayoutDaylight     applyLayoutDaylight
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+as.binary               as.binary
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+as.data.frame.phylo     as.data.frame
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+as.polytomy             as.polytomy
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+collapse                collapse
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+decimal2Date            decimal2Date
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+download.phylopic       download.phylopic
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+expand                  expand
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+facet_plot              facet_plot
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+flip                    flip
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+fortify.phylo           fortify
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+geom_aline              geom_aline
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+geom_balance            geom_balance
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+geom_cladelabel         geom_cladelabel
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+geom_cladelabel2        geom_cladelabel2
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+geom_hilight            geom_hilight
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+geom_hilight_encircle   geom_hilight_encircle
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+geom_label2             geom_label2
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+geom_nodepoint          geom_nodepoint
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+geom_point2             geom_point2
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+geom_range              geom_range
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+geom_rootpoint          geom_rootpoint
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+geom_segment2           geom_segment2
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+geom_strip              geom_strip
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+geom_taxalink           geom_taxalink
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+geom_text2              geom_text2
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+geom_tiplab             geom_tiplab
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+geom_tiplab2            geom_tiplab2
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+geom_tippoint           geom_tippoint
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+geom_tree               geom_tree
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+geom_tree2              geom_tree2
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+geom_treescale          geom_treescale
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+get.offspring.tip       get.offspring.tip
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+get.path                get.path
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+get.phylopic            get.phylopic
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+getChild.df             getChild.df
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+getNodeAngle.df         getNodeAngle.df
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+getNodeEuclDistances    Get the distances from the node to all other
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+                        nodes in data.frame (including itself if in df)
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+getNodesBreadthFirst.df
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+                        getNodesBreadthFirst.df
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+getParent.df            getParent.df
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+getSubtree              getSubtree
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+getSubtree.df           getSubtree.df
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+getSubtreeUnrooted      getSubtreeUnrooted
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+getSubtreeUnrooted.df   getSubtreeUnrooted
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+getTreeArcAngles        getTreeArcAngles
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+get_balance_position    get_balance_position
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+get_clade_position      get_clade_position
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+get_heatmap_column_position
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+                        get_heatmap_column_position
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+get_taxa_name           get_taxa_name
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+ggtree                  visualizing phylogenetic tree and heterogenous
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+                        associated data based on grammar of graphics
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+                        'ggtree' provides functions for visualizing
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+                        phylogenetic tree and its associated data in R.
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+gheatmap                gheatmap
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+groupClade              groupClade method
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+groupOTU                groupOTU method
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+gzoom                   gzoom method
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+gzoom.phylo             gzoom
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+identify.gg             identify
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+inset                   inset
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+layoutDaylight          Equal daylight layout method for unrooted
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+                        trees.
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+layoutEqualAngle        layoutEqualAngle
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+msaplot                 msaplot
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+multiplot               multiplot
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+nodebar                 nodebar
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+nodeid                  nodeid
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+nodepie                 nodepie
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+open_tree               open_tree
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+phylopic                phylopic
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+print.beastList         print
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+reroot                  reroot method
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+rescale_tree            rescale_tree
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+revts                   revts
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+rm.singleton.newick     rm.singleton.newick
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+rotate                  rotate
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+rotateTreePoints.df     rotateTreePoints.data.fram
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+rotate_tree             rotate_tree
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+scaleClade              scaleClade
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+scale_color             scale_color method
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+scale_x_ggtree          scale_x_ggtree
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+stat_balance            stat_balance
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+stat_chull              stat_chull
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+stat_hilight            stat_hilight
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+subview                 subview
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+theme_inset             theme_inset
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+theme_transparent       theme_transparent
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+theme_tree              theme_tree
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+theme_tree2             theme_tree2
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+viewClade               viewClade
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+xlim_expand             xlim_expand
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+xlim_tree               xlim_tree
ggtree/Meta/Rd.rds
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ggtree/Meta/hsearch.rds
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ggtree/Meta/links.rds
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ggtree/Meta/nsInfo.rds
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ggtree/Meta/package.rds
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ggtree/NAMESPACE
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+# Generated by roxygen2: do not edit by hand
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+
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+S3method(as.binary,phylo)
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+S3method(as.data.frame,phylo)
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+S3method(as.data.frame,treedata)
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+S3method(fortify,beast)
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+S3method(fortify,codeml)
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+S3method(fortify,codeml_mlc)
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+S3method(fortify,hyphy)
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+S3method(fortify,jplace)
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+S3method(fortify,multiPhylo)
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+S3method(fortify,obkData)
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+S3method(fortify,paml_rst)
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+S3method(fortify,phangorn)
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+S3method(fortify,phylip)
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+S3method(fortify,phylo)
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+S3method(fortify,phylo4)
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+S3method(fortify,phylo4d)
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+S3method(fortify,phyloseq)
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+S3method(fortify,r8s)
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+S3method(fortify,treedata)
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+S3method(identify,gg)
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+S3method(print,beastList)
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+export("%+>%")
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+export("%<%")
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+export("%<+%")
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+export("%>%")
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+export(.)
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+export(Date2decimal)
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+export(GeomHilight)
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+export(MRCA)
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+export(StatBalance)
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+export(StatHilight)
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+export(add_colorbar)
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+export(annotation_image)
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+export(apeBoot)
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+export(as.binary)
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+export(as.polytomy)
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+export(collapse)
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+export(decimal2Date)
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+export(download.phylopic)
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+export(expand)
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+export(facet_plot)
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+export(flip)
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+export(geom_aline)
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+export(geom_balance)
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+export(geom_cladelabel)
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+export(geom_cladelabel2)
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+export(geom_hilight)
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+export(geom_hilight_encircle)
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+export(geom_label2)
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+export(geom_nodepoint)
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+export(geom_point2)
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+export(geom_range)
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+export(geom_rootpoint)
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+export(geom_segment2)
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+export(geom_strip)
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+export(geom_taxalink)
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+export(geom_text2)
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+export(geom_tiplab)
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+export(geom_tiplab2)
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+export(geom_tippoint)
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+export(geom_tree)
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+export(geom_tree2)
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+export(geom_treescale)
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+export(get.offspring.tip)
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+export(get.path)
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+export(get.phylopic)
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+export(get_balance_position)
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+export(get_clade_position)
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+export(get_heatmap_column_position)
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+export(get_taxa_name)
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+export(ggtree)
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+export(gheatmap)
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+export(gzoom)
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+export(inset)
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+export(msaplot)
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+export(multiplot)
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+export(nodebar)
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+export(nodeid)
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+export(nodepie)
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+export(open_tree)
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+export(phylopic)
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+export(reroot)
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+export(rescale_tree)
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+export(revts)
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+export(rotate)
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+export(rotate_tree)
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+export(scaleClade)
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+export(scale_color)
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+export(scale_x_ggtree)
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+export(stat_balance)
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+export(stat_chull)
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+export(stat_hilight)
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+export(subview)
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+export(theme_inset)
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+export(theme_transparent)
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+export(theme_tree)
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+export(theme_tree2)
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+export(viewClade)
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+export(xlim_expand)
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+export(xlim_tree)
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+exportMethods(groupClade)
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+exportMethods(groupOTU)
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+exportMethods(gzoom)
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+exportMethods(reroot)
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+exportMethods(scale_color)
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+importFrom(ape,di2multi)
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+importFrom(ape,extract.clade)
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+importFrom(ape,getMRCA)
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+importFrom(ape,is.binary.tree)
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+importFrom(ape,ladderize)
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+importFrom(ape,read.tree)
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+importFrom(ape,reorder.phylo)
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+importFrom(ape,write.tree)
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+importFrom(ggplot2,Geom)
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+importFrom(ggplot2,GeomCurve)
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+importFrom(ggplot2,GeomLabel)
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+importFrom(ggplot2,GeomPoint)
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+importFrom(ggplot2,GeomRect)
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+importFrom(ggplot2,GeomSegment)
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+importFrom(ggplot2,GeomText)
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+importFrom(ggplot2,Stat)
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+importFrom(ggplot2,aes)
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+importFrom(ggplot2,aes_)
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+importFrom(ggplot2,aes_string)
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+importFrom(ggplot2,annotate)
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+importFrom(ggplot2,annotation_custom)
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+importFrom(ggplot2,coord_cartesian)
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+importFrom(ggplot2,coord_flip)
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+importFrom(ggplot2,coord_polar)
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+importFrom(ggplot2,draw_key_path)
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+importFrom(ggplot2,draw_key_point)
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+importFrom(ggplot2,draw_key_text)
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+importFrom(ggplot2,element_blank)
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+importFrom(ggplot2,element_line)
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+importFrom(ggplot2,element_rect)
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+importFrom(ggplot2,facet_grid)
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+importFrom(ggplot2,fortify)
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+importFrom(ggplot2,geom_bar)
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+importFrom(ggplot2,geom_blank)
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+importFrom(ggplot2,geom_rect)
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+importFrom(ggplot2,geom_segment)
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+importFrom(ggplot2,geom_text)
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+importFrom(ggplot2,geom_tile)
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+importFrom(ggplot2,ggplot)
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+importFrom(ggplot2,ggplotGrob)
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+importFrom(ggplot2,ggplot_build)
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+importFrom(ggplot2,ggproto)
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+importFrom(ggplot2,guide_legend)
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+importFrom(ggplot2,guides)
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+importFrom(ggplot2,last_plot)
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+importFrom(ggplot2,layer)
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+importFrom(ggplot2,position_nudge)
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+importFrom(ggplot2,scale_color_manual)
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+importFrom(ggplot2,scale_fill_discrete)
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+importFrom(ggplot2,scale_fill_gradient)
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+importFrom(ggplot2,scale_fill_manual)
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+importFrom(ggplot2,scale_x_continuous)
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+importFrom(ggplot2,scale_x_date)
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+importFrom(ggplot2,scale_x_reverse)
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+importFrom(ggplot2,scale_y_continuous)
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+importFrom(ggplot2,theme)
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+importFrom(ggplot2,theme_bw)
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+importFrom(ggplot2,xlab)
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+importFrom(ggplot2,xlim)
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+importFrom(ggplot2,ylab)
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+importFrom(ggplot2,ylim)
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+importFrom(grDevices,col2rgb)
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+importFrom(grDevices,colorRampPalette)
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+importFrom(grDevices,rgb)
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+importFrom(graphics,identify)
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+importFrom(grid,convertX)
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+importFrom(grid,convertY)
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+importFrom(grid,dataViewport)
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+importFrom(grid,grid.layout)
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+importFrom(grid,grid.locator)
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+importFrom(grid,grid.newpage)
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+importFrom(grid,pushViewport)
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+importFrom(grid,rasterGrob)
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+importFrom(grid,unit)
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+importFrom(grid,viewport)
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+importFrom(magrittr,"%<>%")
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+importFrom(magrittr,"%>%")
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+importFrom(magrittr,add)
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+importFrom(magrittr,equals)
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+importFrom(methods,is)
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+importFrom(methods,missingArg)
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+importFrom(rvcheck,get_fun_from_pkg)
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+importFrom(tidyr,gather)
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+importFrom(treeio,as.phylo)
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+importFrom(treeio,as.treedata)
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+importFrom(treeio,get.placements)
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+importFrom(treeio,groupClade)
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+importFrom(treeio,groupOTU)
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+importFrom(utils,download.file)
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+importFrom(utils,modifyList)
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+importFrom(utils,packageDescription)
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+importFrom(utils,packageVersion)
ggtree/NEWS
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+CHANGES IN VERSION 1.9.1
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+------------------------
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+ o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>
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+ o geom_cladelabel support `angle="auto"` for circular layout tree <2017-05-05, Fri>
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+
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+CHANGES IN VERSION 1.8.0
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+------------------------
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+ o BioC 3.5 release <2017-04-26, Wed>
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+
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+CHANGES IN VERSION 1.7.11
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+------------------------
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+ o remove layout.method parameter <2017-04-20, Thu>
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+   + https://github.com/GuangchuangYu/ggtree/issues/118#issuecomment-295130818
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+   + https://github.com/GuangchuangYu/ggtree/issues/125
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+
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+CHANGES IN VERSION 1.7.10
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+------------------------
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+ o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>
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+   + will be defunct in version >= 1.9.0
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+   + user should use ggimage package to annotate tree with graphic object or image file
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+ o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon>
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+
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+CHANGES IN VERSION 1.7.9
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+------------------------
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+ o fixed geom_range to support height_0.95_HPD <2017-03-03, Fri>
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+ o fixed geom_tiplab(geom='label') <2017-03-02, Thu>
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+   + https://github.com/GuangchuangYu/ggtree/issues/115
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+
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+CHANGES IN VERSION 1.7.8
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+------------------------
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+ o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed>
32 
+ o unrooted layout support branch.length="none", fixed #114 <2017-03-01, Wed>
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+ o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>
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+
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+CHANGES IN VERSION 1.7.7
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+------------------------
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+ o supports parse="emoji" in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2 <2017-02-16, Thu>
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+ o aes(subset) now support logical vector contains NA <2017-02-16, Thu>
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+ o add legend transparency to theme_transparent <2017-02-13, Mon>
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+   + <https://github.com/GuangchuangYu/ggtree/pull/112>
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+ o update citation info <2017-01-20, Fri>
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+
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+CHANGES IN VERSION 1.7.6
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+------------------------
45 
+ o inset support reverse scale <2017-01-05, Thu>
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+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/_JPfm71Z8nM/6gL93oxHFQAJ
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+
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+CHANGES IN VERSION 1.7.5
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+------------------------
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+ o disable labeling collapsed node as tip <2017-01-03, Tue>
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+   + https://groups.google.com/forum/#!topic/bioc-ggtree/nReqJatMvJQ
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+ o fortify.phylo4d via converting phylo4d to treedata object <2016-12-28, Wed>
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+ o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
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+ o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
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+
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+CHANGES IN VERSION 1.7.4
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+------------------------
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+ o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
59 
+ o now branch.length can set to feature available in phylo4d@data and yscale is supported for phylo4d object <2016-12-06, Tue>
60 
+ o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
61 
+ o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
62 
+ o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
63 
+   + https://github.com/GuangchuangYu/ggtree/issues/98
64 
+ o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
65 
+   + https://groups.google.com/forum/#!topic/bioc-ggtree/Q4LnwoTf1DM
66 
+
67 
+CHANGES IN VERSION 1.7.3
68 
+------------------------
69 
+ o drop.tip method for NHX object <2016-11-11, Fri>
70 
+ o update startup message <2016-11-09, Wed>
71 
+ o reverse timescale x-axis <2016-11-07, Mon>
72 
+   + https://github.com/GuangchuangYu/ggtree/issues/87
73 
+
74 
+CHANGES IN VERSION 1.7.2
75 
+------------------------
76 
+ o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
77 
+ o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
78 
+   + xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
79 
+ o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
80 
+   + https://github.com/GuangchuangYu/ggtree/issues/84
81 
+
82 
+CHANGES IN VERSION 1.7.1
83 
+------------------------
84 
+ o xlim_tree layer and test <2016-10-31, Mon>
85 
+   + set x axis limits for Tree panel for facet_plot
86 
+ o update read.nhx <2016-10-30, Sun>
87 
+   + add tip numbers to @nhx_tags and add tests
88 
+   + https://github.com/GuangchuangYu/ggtree/pull/83
89 
+   + store nhx_tags$node as numeric values <2016-10-31, Mon>
90 
+ o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
91 
+   + https://github.com/tengfei/ggbio/issues/83
92 
+ o make tree stats available in facet_plot <2016-10-24, Mon>
93 
+
94 
+CHANGES IN VERSION 1.6.0
95 
+------------------------
96 
+ o BioC 3.4 released <2016-10-18, Tue>
97 
+
98 
+CHANGES IN VERSION 1.5.17
99 
+------------------------
100 
+ o read.nhx support newick file <2016-10-17, Mon>
101 
+   + https://github.com/GuangchuangYu/ggtree/issues/79
102 
+
103 
+CHANGES IN VERSION 1.5.16
104 
+------------------------
105 
+ o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>
106 
+   + https://www.biostars.org/p/210401/#216128
107 
+ o fixed aes mapping in geom_strip <2016-10-11, Tue>
108 
+ o fixed R check <2016-10-10, Mon>
109 
+   + check.aes parameter is not available in release version of ggplot2 yet
110 
+
111 
+CHANGES IN VERSION 1.5.15
112 
+------------------------
113 
+ o check.aes for layers defined in ggtree <2016-10-07, Fri>
114 
+ o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
115 
+   + https://github.com/GuangchuangYu/ggtree/issues/78
116 
+
117 
+CHANGES IN VERSION 1.5.14
118 
+------------------------
119 
+ o subset tip in geom_tiplab2 <2016-10-05, Wed>
120 
+ o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
121 
+   + https://github.com/hadley/ggplot2/issues/1797
122 
+ o unit test for groupOTU and groupClade <2016-09-22, Thu>
123 
+ o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
124 
+ o update angle calculation for geom_tiplab <2016-09-13, Thu>
125 
+ 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>
126 
+   + currently only phylo object supported.
127 
+   + add test for as.polytomy
128 
+
129 
+CHANGES IN VERSION 1.5.13
130 
+------------------------
131 
+ o facet_plot for plotting data with tree <2016-09-06, Tue>
132 
+ o more parameters for column names in gheatmap <2016-09-06, Tue>
133 
+   + colnames_angle
134 
+   + colnames_offset_x
135 
+   + colnames_offset_y
136 
+   + hjust
137 
+ o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
138 
+
139 
+CHANGES IN VERSION 1.5.12
140 
+------------------------
141 
+ o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
142 
+ o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
143 
+
144 
+CHANGES IN VERSION 1.5.11
145 
+------------------------
146 
+ o gheatmap works with matrix <2016-08-28, Sun>
147 
+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ
148 
+ o support parsing expression in geom_strip <2016-08-18, Thu>
149 
+ o bug fixed in geom_tiplab <2016-08-17, Wed>
150 
+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
151 
+ o update citation info, add doi. <2016-08-16, Tue>
152 
+
153 
+CHANGES IN VERSION 1.5.10
154 
+------------------------
155 
+ o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
156 
+   + https://github.com/GuangchuangYu/ggtree/issues/72
157 
+
158 
+CHANGES IN VERSION 1.5.9
159 
+------------------------
160 
+ o update citation info <2016-08-12, Fri>
161 
+
162 
+CHANGES IN VERSION 1.5.8
163 
+------------------------
164 
+ o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
165 
+ o geom_cladelabel support parsing expression <2016-08-11, Thu>
166 
+
167 
+CHANGES IN VERSION 1.5.7
168 
+------------------------
169 
+ o geom_strip can accept taxa name as input but labeling strip will not supported.
170 
+   To support labeling strip, user need to input node id  <2016-07-27, Wed>
171 
+ o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
172 
+
173 
+CHANGES IN VERSION 1.5.6
174 
+------------------------
175 
+ o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
176 
+   + still needed for building vignette and for processing FASTA file
177 
+ o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>
178 
+   + the package is still needed if user want to annotate tree with image file
179 
+ o `%<+%` now works with tbl_df <2016-07-21, Thu>
180 
+   + https://github.com/GuangchuangYu/ggtree/issues/66
181 
+ o identify method for ggtree <2016-06-28, Tue>
182 
+   + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
183 
+ o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
184 
+   + see https://github.com/GuangchuangYu/ggtree/pull/64
185 
+
186 
+CHANGES IN VERSION 1.5.5
187 
+------------------------
188 
+ o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
189 
+ o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
190 
+ o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
191 
+   + as.Date won't work for BCE time.
192 
+   + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
193 
+
194 
+CHANGES IN VERSION 1.5.4
195 
+------------------------
196 
+ o reroot method for raxml object <2016-05-22, Sun>
197 
+ o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
198 
+ o bug fixed in collapse <2016-05-20, Fri>
199 
+   + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
200 
+ o use byte compiler <2016-05-18, Wed>
201 
+ o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
202 
+ o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
203 
+
204 
+CHANGES IN VERSION 1.5.3
205 
+------------------------
206 
+ o add examples in vignettes <2016-05-13, Fri>
207 
+   + add fan layout example in treeVisualization vignette
208 
+   + add open_tree and rotate_tree example in treeManipulation vignette
209 
+ o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
210 
+ o rotate_tree and open_tree function <2016-05-12, Thu>
211 
+ o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
212 
+ o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
213 
+
214 
+CHANGES IN VERSION 1.5.2
215 
+------------------------
216 
+ o add multiplot in ggtreeUtilities vignette <2016-05-12, Thu>
217 
+ o add example of integrate user's data using phylo4d in treeAnnotation vignette <2016-05-11, Wed>
218 
+ o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>
219 
+ o geom_hilight now supports hilight tips <2016-05-10, Tue>
220 
+   + https://github.com/GuangchuangYu/ggtree/issues/53
221 
+ o more accurate ylim & angle for circular layout <2016-05-10, Tue>
222 
+   + https://github.com/GuangchuangYu/ggtree/issues/40
223 
+ o supports phylo4d object <2016-05-10, Tue>
224 
+   + https://github.com/GuangchuangYu/ggtree/issues/47
225 
+
226 
+CHANGES IN VERSION 1.5.1
227 
+------------------------
228 
+ o update vignettes <2016-05-10, Tue>
229 
+   + add geom_range example in treeImport
230 
+   + add geom_strip and geom_taxalink example in treeAnnotation
231 
+   + add ggtreeUtilities vignette
232 
+ o gheatmap now works with data.frame of only one column <2016-05-09, Mon>
233 
+   + contributed by Justin Silverman <jsilve24@gmail.com>
234 
+   + https://github.com/GuangchuangYu/ggtree/pull/57
235 
+ o geom_strip for associated taxa <2016-05-09, Mon>
236 
+   + https://github.com/GuangchuangYu/ggtree/issues/52
237 
+
238 
+CHANGES IN VERSION 1.4.0
239 
+------------------------
240 
+ o BioC 3.3 released <2016-05-05, Thu>
241 
+
242 
+CHANGES IN VERSION 1.3.16
243 
+------------------------
244 
+ o geom_treescale() supports family argument <2016-04-27, Wed>
245 
+   + https://github.com/GuangchuangYu/ggtree/issues/56
246 
+ o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu>
247 
+   + https://github.com/GuangchuangYu/ggtree/issues/54
248 
+ o support passing textConnection(text_string) as a file <2016-04-21, Thu>
249 
+   + contributed by Casey Dunn <casey_dunn@brown.edu>
250 
+   + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693
251 
+
252 
+CHANGES IN VERSION 1.3.15
253 
+------------------------
254 
+ o geom_tiplab2 supports parameter hjust <2016-04-18, Mon>
255 
+ o geom_tiplab and geom_tiplab2 support using geom_label2 by passing geom="label" <2016-04-07, Thu>
256 
+ o geom_label2 that support subsetting <2016-04-07, Thu>
257 
+ o geom_tiplab2 for adding tip label of circular layout <2016-04-06, Wed>
258 
+ o use plot$plot_env to access ggplot2 parameter <2016-04-06, Wed>
259 
+ o geom_taxalink for connecting related taxa <2016-04-01, Fri>
260 
+ o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>
261 
+
262 
+CHANGES IN VERSION 1.3.14
263 
+------------------------
264 
+ o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>
265 
+ o update theme_tree2 due to the issue of https://github.com/hadley/ggplot2/issues/1567 <2016-03-05, Sat>
266 
+ o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
267 
+   + see https://github.com/GuangchuangYu/ggtree/issues/46
268 
+ o subview and inset now supports annotating with img files <2016-02-23, Tue>
269 
+
270 
+CHANGES IN VERSION 1.3.13
271 
+------------------------
272 
+ o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
273 
+ o geom_cladelabel works with collapse <2016-02-07, Sun>
274 
+   + see https://github.com/GuangchuangYu/ggtree/issues/38
275 
+
276 
+CHANGES IN VERSION 1.3.12
277 
+------------------------
278 
+ o exchange function name of geom_tree and geom_tree2  <2016-01-25, Mon>
279 
+ o solved issues of geom_tree2 <2016-01-25, Mon>
280 
+   + https://github.com/hadley/ggplot2/issues/1512
281 
+ o colnames_level parameter in gheatmap <2016-01-25, Mon>
282 
+ o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
283 
+
284 
+CHANGES IN VERSION 1.3.11
285 
+------------------------
286 
+ o solved issues of geom_tree2 <2016-01-25, Mon>
287 
+   + https://github.com/GuangchuangYu/ggtree/issues/36
288 
+ o change compute_group() to compute_panel in geom_tree2() <2016-01-21, Thu>
289 
+   + fixed issue, https://github.com/GuangchuangYu/ggtree/issues/36
290 
+ o support phyloseq object <2016-01-21, Thu>
291 
+ o update geom_point2, geom_text2 and geom_segment2 to support setup_tree_data <2016-01-21, Thu>
292 
+ o implement geom_tree2 layer that support duplicated node records via the setup_tree_data function <2016-01-21, Thu>
293 
+ o rescale_tree function for rescaling branch length of tree object <2016-01-20, Wed>
294 
+ o upgrade set_branch_length, now branch can be rescaled using feature in extraInfo slot <2016-01-20, Wed>
295 
+
296 
+CHANGES IN VERSION 1.3.10
297 
+------------------------
298 
+ o remove dependency of gridExtra by implementing multiplot function instead of using grid.arrange <2016-01-20, Wed>
299 
+ o remove dependency of colorspace <2016-01-20, Wed>
300 
+ o support phylip tree format and update vignette of phylip example <2016-01-15, Fri>
301 
+
302 
+CHANGES IN VERSION 1.3.9
303 
+------------------------
304 
+ o optimize getYcoord <2016-01-14, Thu>
305 
+ o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>
306 
+ o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.
307 
+   these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>
308 
+   + > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.
309 
+
310 
+CHANGES IN VERSION 1.3.8
311 
+------------------------
312 
+ o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
313 
+ o add viewClade function <2016-01-12, Tue>
314 
+ o support obkData object defined by OutbreakTools <2016-01-12, Tue>
315 
+ o update vignettes <2016-01-07, Thu>
316 
+ o 05 advance tree annotation vignette <2016-01-04, Mon>
317 
+ o export theme_inset <2016-01-04, Mon>
318 
+ o inset, nodebar, nodepie functions <2015-12-31, Thu>
319 
+
320 
+CHANGES IN VERSION 1.3.7
321 
+------------------------
322 
+ o split the long vignette to several vignettes
323 
+   + 00 ggtree <2015-12-29, Tue>
324 
+   + 01 tree data import <2015-12-28, Mon>
325 
+   + 02 tree visualization <2015-12-28, Mon>
326 
+   + 03 tree manipulation <2015-12-28, Mon>
327 
+   + 04 tree annotation <2015-12-29, Tue>
328 
+
329 
+CHANGES IN VERSION 1.3.6
330 
+------------------------
331 
+ o MRCA function for finding Most Recent Common Ancestor among a vector of tips <2015-12-22, Tue>
332 
+ o geom_cladelabel: add bar and label to annotate a clade <2015-12-21, Mon>
333 
+   - remove annotation_clade and annotation_clade2 functions.
334 
+ o geom_treescale: tree scale layer. (add_legend was removed) <2015-12-21, Mon>
335 
+
336 
+CHANGES IN VERSION 1.3.5
337 
+------------------------
338 
+ o bug fixed, read.nhx now works with scientific notation <2015-11-30, Mon>
339 
+   + see https://github.com/GuangchuangYu/ggtree/issues/30
340 
+
341 
+CHANGES IN VERSION 1.3.4
342 
+------------------------
343 
+ o rename beast feature when name conflict with reserve keywords (label, branch, etc) <2015-11-27, Fri>
344 
+ o get_clade_position function <2015-11-26, Thu>
345 
+   + https://github.com/GuangchuangYu/ggtree/issues/28
346 
+ o get_heatmap_column_position function <2015-11-25, Wed>
347 
+   + see https://github.com/GuangchuangYu/ggtree/issues/26
348 
+ o support NHX (New Hampshire X) format via read.nhx function <2015-11-17, Tue>
349 
+ o bug fixed in extract.treeinfo.jplace <2015-11-17, Thu>
350 
+
351 
+CHANGES IN VERSION 1.3.3
352 
+------------------------
353 
+ o support color=NULL in gheatmap, then no colored line will draw within the heatmap <2015-10-30, Fri>
354 
+ o add `angle` for also rectangular, so that it will be available for layout='rectangular' following by coord_polar() <2015-10-27, Tue>
355 
+
356 
+CHANGES IN VERSION 1.3.2
357 
+------------------------
358 
+ o update vignette, add example of ape bootstrap and phangorn ancestral sequences <2015-10-26, Mon>
359 
+ o add support of ape bootstrap analysis <2015-10-26, Mon>
360 
+   see https://github.com/GuangchuangYu/ggtree/issues/20
361 
+ o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon>
362 
+   see https://github.com/GuangchuangYu/ggtree/issues/21
363 
+
364 
+CHANGES IN VERSION 1.3.1
365 
+------------------------
366 
+ o change angle to angle + 90, so that label will in radial direction <2015-10-22, Thu>
367 
+   + see https://github.com/GuangchuangYu/ggtree/issues/17
368 
+ o na.rm should be always passed to layer(), fixed it in geom_hilight and geom_text2 <2015-10-21, Wed>
369 
+   + see https://github.com/hadley/ggplot2/issues/1380
370 
+ o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>
371 
+
372 
+CHANGES IN VERSION 1.2.0
373 
+------------------------
374 
+ o BioC 3.2 released
375 
+
376 
+CHANGES IN VERSION 1.1.21
377 
+------------------------
378 
+ o support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>
379 
+ o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
380 
+ o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
381 
+
382 
+CHANGES IN VERSION 1.1.20
383 
+------------------------
384 
+ o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
385 
+ o bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>
386 
+ o update vignette by adding r8s example <2015-09-02, Wed>
387 
+ o defined r8s class, see http://loco.biosci.arizona.edu/r8s/  <2015-09-02, Wed>
388 
+   + add r8s sample files
389 
+   + read.r8s, parser function
390 
+   + fortify method
391 
+   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
392 
+ o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
393 
+ o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
394 
+ o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
395 
+   - remove 'time_scale' parameter.
396 
+ o defined 'raxml' class for RAxML bootstrapping analysis result <2015-09-01, Tue>
397 
+   + see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
398 
+   + read.raxml, parser function
399 
+   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
400 
+   + fortify.raxml method
401 
+ o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
402 
+
403 
+CHANGES IN VERSION 1.1.19
404 
+------------------------
405 
+ o use fortify instead of fortify.phylo in fortify.multiPhylo,
406 
+   so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
407 
+ o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
408 
+ o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
409 
+   + these two packages is not commonly used, and will be loaded automatically when needed.
410 
+
411 
+CHANGES IN VERSION 1.1.18
412 
+------------------------
413 
+ o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
414 
+     'unroot' is not changed. <2015-08-28. Fri>
415 
+ o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri>
416 
+     see https://github.com/hadley/ggplot2/issues/1295
417 
+ o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
418 
+ o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
419 
+
420 
+CHANGES IN VERSION 1.1.17
421 
+------------------------
422 
+ o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
423 
+ o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
424 
+ o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
425 
+ o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
426 
+ o theme_transparent to make background transparent <2015-08-27, Thu>
427 
+ o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
428 
+
429 
+CHANGES IN VERSION 1.1.16
430 
+------------------------
431 
+ o update citation <2015-08-17, Mon>
432 
+
433 
+CHANGES IN VERSION 1.1.15
434 
+------------------------
435 
+ o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>
436 
+ o support changing size of add_legend <2015-08-13, Thu>
437 
+ o reroot methods for phylo and beast <2015-08-07, Fri>
438 
+
439 
+CHANGES IN VERSION 1.1.14
440 
+------------------------
441 
+ o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>
442 
+
443 
+CHANGES IN VERSION 1.1.13
444 
+------------------------
445 
+ o implement annotation_image <2015-08-01, Sat>
446 
+ o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
447 
+ o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
448 
+
449 
+CHANGES IN VERSION 1.1.12
450 
+------------------------
451 
+ o update vignette according to the changes <2015-07-31, Fri>
452 
+ o add mapping parameter in ggtree function <2015-07-31, Fri>
453 
+ o extend groupClade to support operating on tree view <2015-07-31, Fri>
454 
+ o extend groupOTU to support operating on tree view <2015-07-31, Fri>
455 
+ o new implementation of groupClade & groupOTU <2015-07-31, Fri>
456 
+
457 
+CHANGES IN VERSION 1.1.11
458 
+------------------------
459 
+ o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
460 
+ o better add_legend implementation. <2015-07-30, Thu>
461 
+ o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
462 
+ o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
463 
+
464 
+CHANGES IN VERSION 1.1.10
465 
+------------------------
466 
+ o solve overlapping branches for layout = "fan" || "radial",
467 
+   that are coord_polar-ized layouts.
468 
+   see https://github.com/GuangchuangYu/ggtree/issues/6,
469 
+   contributed by Vincent Bonhomme. <2015-07-22, Wed>
470 
+
471 
+CHANGES IN VERSION 1.1.9
472 
+------------------------
473 
+ o update add_legend to align legend text <2015-07-06, Mon>
474 
+ o bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed>
475 
+ o rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed>
476 
+ o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
477 
+ o add example of flip function in vignette <2015-06-30, Tue>
478 
+ o flip function for exchanging positions of two selected branches <2015-06-30, Tue>
479 
+
480 
+CHANGES IN VERSION 1.1.8
481 
+------------------------
482 
+ o update get.placement <2015-06-05, Fri>
483 
+ o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
484 
+ o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
485 
+ o add mask function <2015-06-02, Tue>
486 
+
487 
+CHANGES IN VERSION 1.1.7
488 
+------------------------
489 
+ o add example of msaplot in vignette <2015-05-22, Fri>
490 
+ o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
491 
+
492 
+CHANGES IN VERSION 1.1.6
493 
+------------------------
494 
+ o add vertical_only parameter to scaleClade and set to TRUE by default.
495 
+   only vertical will be scaled by default. <2015-05-22, Fri>
496 
+ o update add_colorbar & add_legend <2015-05-21, Thu>
497 
+ o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
498 
+ o gheatmap implementation of gplot <2015-05-18, Mon>
499 
+ o add_legend for adding evolution distance legend <2015-05-18, Mon>
500 
+
501 
+CHANGES IN VERSION 1.1.5
502 
+------------------------
503 
+ o implement scaleClade <2015-05-12, Tue>
504 
+
505 
+CHANGES IN VERSION 1.1.4
506 
+------------------------
507 
+ o better performance of parsing beast tree  <2015-05-11, Mon>
508 
+   + support beast tree begin with 'tree tree_1 = ' and other forms.
509 
+   + support file that only contains one evidence for some of the nodes/tips
510 
+ o update add_colorbar to auto determine the position <2015-05-04, Mon>
511 
+ o add_colorbar function <2015-04-30, Thu>
512 
+
513 
+CHANGES IN VERSION 1.1.3
514 
+------------------------
515 
+ o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
516 
+ o remove slash line in heatmap legend <2015-04-30, Thu>
517 
+ o update vignette to add example of merge_tree <2015-04-29, Wed>
518 
+
519 
+CHANGES IN VERSION 1.1.2
520 
+------------------------
521 
+ o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
522 
+ o add examples folder in inst that contains sample data <2015-04-29, Wed>
523 
+ o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
524 
+ o add line break if substitution longer than 50 character <2015-04-28, Tue>
525 
+ o support calculating branch for time scale tree <2015-04-28, Tue>
526 
+ o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
527 
+ o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
528 
+ o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue>
529 
+ o extend fortify methods to support additional fields <2015-04-28, Tue>
530 
+ o extend get.fields methods to support additional fields <2015-04-28, Tue>
531 
+ o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
532 
+ o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
533 
+
534 
+CHANGES IN VERSION 1.1.1
535 
+------------------------
536 
+ o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
537 
+ o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
538 
+ o add Tommy in author <2015-04-27, Mon>
539 
+
540 
+CHANGES IN VERSION 0.99.28
541 
+------------------------
542 
+ o update vignette with floating table of content <2015-04-08, Wed>
543 
+
544 
+CHANGES IN VERSION 0.99.27
545 
+------------------------
546 
+ o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>
547 
+
548 
+CHANGES IN VERSION 0.99.26
549 
+------------------------
550 
+ o update geom_tiplab <2015-03-31, Tue>
551 
+ o update plot method of beast <2015-03-17, Tue>
552 
+
553 
+CHANGES IN VERSION 0.99.25
554 
+------------------------
555 
+ o implement groupClade <2015-03-13, Fri>
556 
+
557 
+CHANGES IN VERSION 0.99.24
558 
+------------------------
559 
+ o use "round" segment end, look very better <2015-03-12, Thu>
560 
+ o update vignett <2015-03-11, Wed>
561 
+
562 
+CHANGES IN VERSION 0.99.23
563 
+------------------------
564 
+ o mv geom_hilight to hilight <2015-03-11, Wed>
565 
+ o mv geom_phylopic to phylopic <2015-03-11, Wed>
566 
+ o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
567 
+
568 
+CHANGES IN VERSION 0.99.22
569 
+------------------------
570 
+ o remove quote in beast tip/node labels <2015-03-10, Tue>
571 
+
572 
+CHANGES IN VERSION 0.99.21
573 
+------------------------
574 
+ o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
575 
+
576 
+CHANGES IN VERSION 0.99.19
577 
+------------------------
578 
+ o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>
579 
+
580 
+CHANGES IN VERSION 0.99.18
581 
+------------------------
582 
+ o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
583 
+
584 
+CHANGES IN VERSION 0.99.17
585 
+------------------------
586 
+ o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
587 
+
588 
+CHANGES IN VERSION 0.99.16
589 
+------------------------
590 
+ o correct typo in vignette <2015-02-10, Tue>
591 
+
592 
+CHANGES IN VERSION 0.99.15
593 
+------------------------
594 
+ o fully support of replace operator, %<% <2015-02-09, Mon>
595 
+
596 
+CHANGES IN VERSION 0.99.14
597 
+------------------------
598 
+ o add example in groupOTU for adding legend manually <2015-02-09, Mon>.
599 
+
600 
+CHANGES IN VERSION 0.99.13
601 
+------------------------
602 
+ o two dimensional tree <2015-02-06, Fri>
603 
+
604 
+CHANGES IN VERSION 0.99.12
605 
+------------------------
606 
+ o update vignette <2015-02-04, Wed>
607 
+ o gzoom methods that supports all tree objects <2015-02-04, Wed>
608 
+ o geom_hilight layer for highlighting clade <2015-02-04, Wed>
609 
+
610 
+CHANGES IN VERSION 0.99.11
611 
+------------------------
612 
+ o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
613 
+ o revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed>
614 
+
615 
+CHANGES IN VERSION 0.99.10
616 
+------------------------
617 
+ o support y scale by category variable <2015-02-03, Tue>
618 
+ o support order nodes by yscale <2015-02-03, Tue>
619 
+
620 
+CHANGES IN VERSION 0.99.9
621 
+------------------------
622 
+ o update vignette <2015-02-02, Mon>
623 
+
624 
+CHANGES IN VERSION 0.99.8
625 
+------------------------
626 
+ o add get.phylopic function to read the online phylo pic and convert it to grob object,
627 
+   which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>
628 
+
629 
+CHANGES IN VERSION 0.99.7
630 
+------------------------
631 
+ o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>
632 
+
633 
+CHANGES IN VERSION 0.99.6
634 
+------------------------
635 
+ o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
636 
+ o now read.beast supports characters in support values <2015-01-18, Sun>
637 
+ o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
638 
+ o implement groupOTU methods <2015-01-14, Wed>
639 
+ o export get.offspring.tip <2015-01-14, Wed>
640 
+
641 
+CHANGES IN VERSION 0.99.5
642 
+------------------------
643 
+ o move ape and ggplot2 from Depends to Imports <2015-01-12, Mon>
644 
+ o get.tipseq method for paml_rst and codeml object <2015-01-08, Thu>
645 
+ o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
646 
+ o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
647 
+ o remove <<- and update vignette <2015-01-06, Tue>
648 
+ o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
649 
+ o update cladogram layout <2015-01-05, Mon>
650 
+ o read.baseml function and update vignette with baseml example <2015-01-04, Sun>
651 
+ o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
652 
+ o merge all vignettes to ggtree vignette <2015-01-04, Sun>
653 
+
654 
+CHANGES IN VERSION 0.99.4
655 
+------------------------
656 
+ o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
657 
+ o get.subs method for hyphy object <2015-01-03, Sat>
658 
+ o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
659 
+ o export read.hyphy <2015-01-02, Fri>
660 
+ o export hyphy class <2015-01-01, Thu>
661 
+ o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
662 
+ o show, get.fields, get.subs and plot methods for codeml class <2014-12-30, Tue>
663 
+ o plot method for paml_rst class <2014-12-30, Tue>
664 
+ o get.subs, method for paml_rst class <2014-12-30, Tue>
665 
+ o show, plot, get.tree and fority methods for codeml_mlc class <2014-12-29, Mon>
666 
+ o codeml class <2014-12-29, Mon>
667 
+ o hyphy class and read.hyphy prototype <2014-12-27, Sat>
668 
+ o update man file and add example file of beast output <2014-12-26, Fri>
669 
+ o get.tree and get.fileds methods of beast class <2014-12-26, Fri>
670 
+ o read.beast <2014-12-26, Fri>
671 
+ o beast class and show method <2014-12-26, Fri>
672 
+ o coplot prototype<2014-12-24, Wed>
673 
+ o parse translation matrix in beast nexus <2014-12-24, Wed>
674 
+ o extract beast stats info <2014-12-23, Tue>
675 
+
676 
+CHANGES IN VERSION 0.99.3
677 
+------------------------
678 
+ o gplot function that can view a tree and an associated matrix simultaneously <2014-12-22, Mon>
679 
+ o modified vignette to show based on branch position and break the evolution distance scale <2014-12-22, Mon>
680 
+ o label and annotation can be put based on branch. <2014-12-22, Mon>
681 
+ o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
682 
+ o support unrooted layout in ggplot. <2014-12-21, Sun>
683 
+ o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
684 
+
685 
+CHANGES IN VERSION 0.99.2
686 
+------------------------
687 
+ o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34
688 
+   of 'Inferring Phylogenies' (page 578-580) <2014-12-20, Sat>
689 
+ o add layout parameter in ggtree and geom_tree, now supports phylogram and cladogram <2014-12-20, Sat>
690 
+ o %<+% function for inserting annotation data to a tree view <2014-12-20, Sat>
691 
+ o update ggtree-treeAnnotation vignette <2014-12-20, Sat>
692 
+
693 
+CHANGES IN VERSION 0.99.1
694 
+------------------------
695 
+ o %<% function for updating tree view with a new tree <2014-12-19, Fri>
696 
+ o add examples in man files <2014-12-19, Fri>
697 
+
698 
+CHANGES IN VERSION 0.2.3
699 
+------------------------
700 
+ o add README.md <2014-12-19, Fri>
701 
+ o update ggtree-treeViewer vignette <2014-12-19, Fri>
702 
+ o use BiocStyle in vignette <2014-12-19, Fri>
703 
+ o geom_nplace and geom_place layer <2014-12-18, Thu>
704 
+ o add theme_tree2 theme for showing evolution distance <2014-12-18, Thu>
705 
+ o rm.singleton.newick now supports internal node like:
706 
+   ((()X, ()Y)Z)AA, in which Z is a singleton. <2014-12-15, Mon>
707 
+
708 
+CHANGES IN VERSION 0.2.2
709 
+------------------------
710 
+ o rm.singleton.newick <2014-12-09, Tue>
711 
+ o as.binary method <2014-12-09, Tue>
712 
+
713 
+CHANGES IN VERSION 0.2.1
714 
+------------------------
715 
+ o geom_eplace <2014-12-07, Sun>
716 
+
717 
+CHANGES IN VERSION 0.2.0
718 
+------------------------
719 
+ o read.jplace to read the jplace file <2014-12-05, Fri>
720 
+ o jplace class for storing information of jplace file <2014-12-05, Fri>
721 
+ o show method of jplace class <2014-12-05, Fri>
722 
+ o get.tree method to get tree from jplace class <2014-12-05, Fri>
723 
+ o extend ggplot2 to support jplace class <2014-12-05, Fri>
724 
+
725 
+CHANGES IN VERSION 0.1.1
726 
+------------------------
727 
+ o add distance legend in ggtree <2014-12-05, Fri>
728 
+
729 
+CHANGES IN VERSION 0.1.0
730 
+------------------------
731 
+ o support ladderize tree <2014-12-05, Fri>
732 
+ o implement geom_tree, geom_tiplab, geom_tippoint, geom_aline and theme_tree <2014-12-04, Thu>
733 
+ o extend ggplot to support phylo object and implement ggtree function <2014-12-04, Thu>
734 
+ o implement fortify function <2014-12-04, Thu>
735 
+ o add getRoot, isRoot and getParent functions <2014-12-03, Wed>
ggtree/R/ggtree
History View file @ 1cfeeff1
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new file mode 100644
... ... 
@@ -0,0 +1,27 @@
1 
+#  File share/R/nspackloader.R
2 
+#  Part of the R package, http://www.R-project.org
3 
+#
4 
+#  Copyright (C) 1995-2012 The R Core Team
5 
+#
6 
+#  This program is free software; you can redistribute it and/or modify
7 
+#  it under the terms of the GNU General Public License as published by
8 
+#  the Free Software Foundation; either version 2 of the License, or
9 
+#  (at your option) any later version.
10 
+#
11 
+#  This program is distributed in the hope that it will be useful,
12 
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
13 
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
14 
+#  GNU General Public License for more details.
15 
+#
16 
+#  A copy of the GNU General Public License is available at
17 
+#  http://www.r-project.org/Licenses/
18 
+
19 
+local({
20 
+    info <- loadingNamespaceInfo()
21 
+    pkg <- info$pkgname
22 
+    ns <- .getNamespace(as.name(pkg))
23 
+    if (is.null(ns))
24 
+        stop("cannot find namespace environment for ", pkg, domain = NA);
25 
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
26 
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
27 
+})
ggtree/R/ggtree.rdb
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ggtree/R/ggtree.rdx
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ggtree/as.phylo.igraph.R
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4 32 
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1 
+
2 
+as.phylo.igraph(x) {
3 
+    edge <- get.edgelist(x)
4 
+
5 
+}
ggtree/examples/FluA_H3_AA.fas
History View file @ 1cfeeff1
0 6 
new file mode 100644
... ... 
@@ -0,0 +1,684 @@
1 
+>A/Swine/Binh_Duong/03_08/2010
2 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPHQILDGGNC
3 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNSENFNWTGVTQNGKSSSCKRGSD
4 
+SSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGVHHPGTYNDQISLYAQASGIITVSTKRNQQTVIPNIGSRRDIP
5 
+SRISIYWTIVKPGDILLINSTGNLIPPRGYFKIQSGRSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
6 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHKNSEGMQAADLKSTQAAINQINGKLNRLIGKT
7 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
8 
+IYHKCDNACIGSIRNGTYDHDIYRDEALNNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
9 
+CI
10 
+>A/Swine/Binh_Duong/03_10/2010
11 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPHQILDGGNC
12 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNSENFNWTGVTQNGKSSSCKRGSD
13 
+SSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGVHHPGTYNDQISLYAQASGIITVSTKRNQQTVIPNIGSRRDIP
14 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGRSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
15 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHKNSEGMQAADLKSTQAAINQINGKLNRLIGKT
16 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
17 
+IYHKCDNACIGSIRNGTYDHDIYRDEALNNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
18 
+CI
19 
+>A/Swine/HK/2503/2011
20 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
21 
+TLIDALLGDPQCDGFQNKKWDLFIERSKAYSNCYPYDVPDYSSLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
22 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPSTYSDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
23 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
24 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
25 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
26 
+IYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
27 
+CI
28 
+>A/Swine/HK_NS2439/2011
29 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
30 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAHSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
31 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPSTYSDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
32 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMISDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
33 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
34 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
35 
+IYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
36 
+CI
37 
+>A/Swine/GX_NS2783/2010
38 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
39 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDMPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
40 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPSTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
41 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
42 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
43 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
44 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
45 
+CI
46 
+>A/Swine/GD/3767/2011
47 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
48 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
49 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
50 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNEKSSIMRSDAPIGKCNSECITPNGSIPNDRPFQNVNRITYGACPR
51 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
52 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
53 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
54 
+CI
55 
+>A/Swine/GX/2242/2011
56 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
57 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
58 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
59 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIGKCNSECITPNGSIPNDRPFQNVNRITYGTCPR
60 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
61 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
62 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFATSCFLLCVVLLGFIMWACQKGNIRCNI
63 
+CI
64 
+>A/Swine/GX/2803/2011
65 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGLCNSPYQILDGGNC
66 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
67 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
68 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
69 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
70 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
71 
+IYHKCDNACIGSIRNGTYDHDVYRDEAFSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
72 
+CI
73 
+>A/Swine/GX_NS3106/2011
74 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGLCNSPYQILDGGNC
75 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
76 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGPRRDIP
77 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
78 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
79 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
80 
+IYHKCDNACIGSIRNGTYDHDVYRDEAFSNRFQIKGVELEAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
81 
+CI
82 
+>A/Swine/GX_NS3108/2011
83 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGLCNSPYQILDGGNC
84 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
85 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
86 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
87 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
88 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
89 
+IYHKCDNACIGSIRNGTYDHDVYRDEAFSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
90 
+CI
91 
+>A/Swine/HK_NS2810/2011
92 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
93 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
94 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGMITVSTKRTQQTVIPNIGSRRDIP
95 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIGKCSSECITPNGSIPNDRPFQNVNRITYGACPR
96 
+YVKQNTLKLATGMRNVPDKQTRGIFGAIAGFIENGWEGMIDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
97 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
98 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
99 
+CI
100 
+>A/Swine/HK/2857/2011
101 
+MKTIIALSYILCLVFAQKFPGNDNSMATLCLGHHAVPNGTMVKTIANDQIEVTNATELVQSSSTGGICNSPHQILDGGNC
102 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYTSLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
103 
+NSFFSRLNWLTHLNYKYPALKVAMPNNEKFDKLYIWGVHHPGTYNDQISLYAQASGIITVSTKRNQQTVIPNIGSRRDIP
104 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPR
105 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAVNQINGKLNRLIGKT
106 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMDKLFERTKKQLRENAEDMGNGCFK
107 
+IYHKCDNACIGSIRNGTYDHDIYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
108 
+CI
109 
+>A/Swine/HK/3238/2011
110 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
111 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
112 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
113 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIGKCNSECITPNGSIPNDRPFQNVNRITYGACPR
114 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
115 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCLK
116 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
117 
+CI
118 
+>A/Swine/HK/3700/2011
119 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
120 
+TLIDAILGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
121 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
122 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIDKCNSECITPNGSIPNDRPFQNVNRITYGACPR
123 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
124 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
125 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
126 
+CI
127 
+>A/Swine/HK/168/2012
128 
+MKTIIALSYILCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQILDGGNC
129 
+TLIDAILGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
130 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
131 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIGKCNSECITPNGSIPNDRPFQNVNRITYGACPR
132 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGVQAADLKSTQAAINQINGKLNRLIGKT
133 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
134 
+IYHKCDNACIGSIRNGTYDHDVYRDEALSNRFQIKGVELKAGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNI
135 
+CI
136 
+>A/Swine/HK/459/2012
137 
+MKTIIALSYIPCLVFAQKFPGNDNNMAMLCLGHHAVPNGTMVKTITNDQIEVTNATELVQSSSTGGICNSPYQVLDGGNC
138 
+TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSIVASSGTLEFNNESFNWTGVTQNGKSASCKRGSD
139 
+NSFFSRLNWLTHLNYKYPALKVTMPNNEKFDKLYIWGAHHPGTYNDQISLYAQASGIITVSTKRTQQTVIPNIGSRRDIP
140 
+SRISIYWTIVKPGDILLINSTGNLIAPRGYFKLQNGKSSIMRSDAPIGKCDSECITPNGSIPNDRPFQNVNRITYGACPR
141 
+YVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGMQAADLKSTQAAINQINGKLNRLIGKT
142 
+NEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFK
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