1. ggtree
  2. R
  3. r8s.R
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
R/r8s.R
History View file @ 14ff9149
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deleted file mode 100644
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-## ##' parse output from r8s
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-## ##'
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-## ##'
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-## ##' @title read.r8s
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-## ##' @param file r8s output log file
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-## ##' @return r8s instance
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-## ##' @export
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-## ##' @author Guangchuang Yu
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-## read.r8s <- function(file) {
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-##     r8s <- readLines(file)
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-##     label_idx <- grep("\\[\\w+\\sDESCRIPTION\\sof\\stree\\s.*\\]", r8s)
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-##     tree_idx <- grep("^tree\\s.*\\s=\\s", r8s)
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-##     if (length(label_idx) != length(tree_idx)) {
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-##         stop("fail to parse the file...")
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-##     }
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-
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-##     tree_text <- gsub("^tree\\s.*\\s=\\s", "", r8s[tree_idx])
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-##     trees <- read.tree(text=tree_text)
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-
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-##     label <- gsub("^\\[(\\w+)\\s.*", "\\1", r8s[label_idx])
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-##     names(trees) <- label
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-
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-##     new("r8s",
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-##         file = filename(file),
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-##         fields = label,
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-##         phylo = trees)
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-## }
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-
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-
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-
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-
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-## ##' @rdname groupClade-methods
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-## ##' @exportMethod groupClade
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-## ##' @param tree which tree selected
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-## setMethod("groupClade", signature(object="r8s"),
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-##           function(object, node, group_name="group", tree="TREE") {
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-##               groupClade_(get.tree(object)[[tree]], node, group_name)
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-##           })
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-
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-## ##' @rdname scale_color-methods
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-## ##' @exportMethod scale_color
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-## ##' @param tree which tree selected
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-## setMethod("scale_color", signature(object="r8s"),
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-##           function(object, by="bootstrap", tree="TREE") {
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-##               scale_color_(get.tree(object)[[tree]], by)
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-##           })
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-
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-
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-## ##' @rdname gzoom-methods
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-## ##' @exportMethod gzoom
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-## ##' @param tree which tree selected
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-## setMethod("gzoom", signature(object="r8s"),
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-##           function(object, focus, subtree=FALSE, widths=c(.3, .7), tree="TREE") {
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-##               gzoom.phylo(get.tree(object)[[tree]], focus, subtree, widths)
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-##           })
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-
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="r8s"),
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-##           function(object,...) {
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-##               object@phylo
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-##           }
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-##           )
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-
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-
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-## ##' @rdname get.fields-methods
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-## ##' @exportMethod get.fields
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-## setMethod("get.fields", signature(object="r8s"),
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-##           function(object, ...) {
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-##               get.fields.tree(object)
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-##           }
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-##           )
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 1 changed files
R/r8s.R
History View file @ 817c093d
... ... 
@@ -1,73 +1,73 @@
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-##' parse output from r8s
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-##'
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-##'
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-##' @title read.r8s
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-##' @param file r8s output log file
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-##' @return r8s instance
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-##' @export
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-##' @author Guangchuang Yu
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-read.r8s <- function(file) {
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-    r8s <- readLines(file)
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-    label_idx <- grep("\\[\\w+\\sDESCRIPTION\\sof\\stree\\s.*\\]", r8s)
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-    tree_idx <- grep("^tree\\s.*\\s=\\s", r8s)
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-    if (length(label_idx) != length(tree_idx)) {
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-        stop("fail to parse the file...")
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-    }
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+## ##' parse output from r8s
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+## ##'
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+## ##'
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+## ##' @title read.r8s
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+## ##' @param file r8s output log file
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+## ##' @return r8s instance
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+## ##' @export
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+## ##' @author Guangchuang Yu
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+## read.r8s <- function(file) {
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+##     r8s <- readLines(file)
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+##     label_idx <- grep("\\[\\w+\\sDESCRIPTION\\sof\\stree\\s.*\\]", r8s)
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+##     tree_idx <- grep("^tree\\s.*\\s=\\s", r8s)
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+##     if (length(label_idx) != length(tree_idx)) {
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+##         stop("fail to parse the file...")
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+##     }
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-    tree_text <- gsub("^tree\\s.*\\s=\\s", "", r8s[tree_idx])
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-    trees <- read.tree(text=tree_text)
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+##     tree_text <- gsub("^tree\\s.*\\s=\\s", "", r8s[tree_idx])
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+##     trees <- read.tree(text=tree_text)
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-    label <- gsub("^\\[(\\w+)\\s.*", "\\1", r8s[label_idx])
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-    names(trees) <- label
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+##     label <- gsub("^\\[(\\w+)\\s.*", "\\1", r8s[label_idx])
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+##     names(trees) <- label
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-    new("r8s",
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-        file = filename(file),
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-        fields = label,
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-        phylo = trees)
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-}
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+##     new("r8s",
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+##         file = filename(file),
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+##         fields = label,
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+##         phylo = trees)
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+## }
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-##' @rdname groupClade-methods
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-##' @exportMethod groupClade
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-##' @param tree which tree selected
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-setMethod("groupClade", signature(object="r8s"),
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-          function(object, node, group_name="group", tree="TREE") {
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-              groupClade_(get.tree(object)[[tree]], node, group_name)
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-          })
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+## ##' @rdname groupClade-methods
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+## ##' @exportMethod groupClade
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+## ##' @param tree which tree selected
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+## setMethod("groupClade", signature(object="r8s"),
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+##           function(object, node, group_name="group", tree="TREE") {
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+##               groupClade_(get.tree(object)[[tree]], node, group_name)
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+##           })
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-##' @rdname scale_color-methods
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-##' @exportMethod scale_color
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-##' @param tree which tree selected
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-setMethod("scale_color", signature(object="r8s"),
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-          function(object, by="bootstrap", tree="TREE") {
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-              scale_color_(get.tree(object)[[tree]], by)
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-          })
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+## ##' @rdname scale_color-methods
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+## ##' @exportMethod scale_color
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+## ##' @param tree which tree selected
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+## setMethod("scale_color", signature(object="r8s"),
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+##           function(object, by="bootstrap", tree="TREE") {
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+##               scale_color_(get.tree(object)[[tree]], by)
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+##           })
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-##' @rdname gzoom-methods
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-##' @exportMethod gzoom
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-##' @param tree which tree selected
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-setMethod("gzoom", signature(object="r8s"),
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-          function(object, focus, subtree=FALSE, widths=c(.3, .7), tree="TREE") {
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-              gzoom.phylo(get.tree(object)[[tree]], focus, subtree, widths)
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-          })
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+## ##' @rdname gzoom-methods
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+## ##' @exportMethod gzoom
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+## ##' @param tree which tree selected
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+## setMethod("gzoom", signature(object="r8s"),
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+##           function(object, focus, subtree=FALSE, widths=c(.3, .7), tree="TREE") {
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+##               gzoom.phylo(get.tree(object)[[tree]], focus, subtree, widths)
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+##           })
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="r8s"),
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-          function(object,...) {
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-              object@phylo
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-          }
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-          )
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="r8s"),
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+##           function(object,...) {
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+##               object@phylo
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+##           }
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+##           )
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-##' @rdname get.fields-methods
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-##' @exportMethod get.fields
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-setMethod("get.fields", signature(object="r8s"),
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-          function(object, ...) {
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-              get.fields.tree(object)
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-          }
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-          )
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+## ##' @rdname get.fields-methods
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+## ##' @exportMethod get.fields
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+## setMethod("get.fields", signature(object="r8s"),
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+##           function(object, ...) {
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+##               get.fields.tree(object)
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+##           }
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+##           )
Browse code

support textConnection

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@116643 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 21/04/2016 11:51:12
Showing 1 changed files
R/r8s.R
History View file @ 0ed2ffd9
... ... 
@@ -21,26 +21,13 @@ read.r8s <- function(file) {
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     names(trees) <- label
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     new("r8s",
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-        file = file,
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+        file = filename(file),
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         fields = label,
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         phylo = trees)
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 }
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-##' @rdname show-methods
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-##' @importFrom ape print.phylo
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-##' @exportMethod show
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-setMethod("show", signature(object = "r8s"),
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-          function(object) {
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-              cat("'r8s' S4 object that stored information of\n\t",
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-                  paste0("'", object@file, "'.\n\n"))
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-              cat("...@ tree: ")
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-              print.phylo(get.tree(object))
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-              ## cat("\nwith the following features available:\n")
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-              ## print_fields(object)
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-          })
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-
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 ##' @rdname groupClade-methods
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 ##' @exportMethod groupClade
Browse code

lots updates

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111813 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/12/2015 04:08:02
Showing 1 changed files
R/r8s.R
History View file @ f1f0d8d2
... ... 
@@ -84,4 +84,3 @@ setMethod("get.fields", signature(object="r8s"),
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               get.fields.tree(object)
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           }
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           )
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-
Browse code

add r8s and raxml support

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109098 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 02/10/2015 06:16:16
Showing 1 changed files
R/r8s.R
History View file @ 75f08f2b
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,87 @@
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+##' parse output from r8s
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+##'
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+##'
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+##' @title read.r8s
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+##' @param file r8s output log file
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+##' @return r8s instance
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+##' @export
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+##' @author Guangchuang Yu
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+read.r8s <- function(file) {
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+    r8s <- readLines(file)
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+    label_idx <- grep("\\[\\w+\\sDESCRIPTION\\sof\\stree\\s.*\\]", r8s)
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+    tree_idx <- grep("^tree\\s.*\\s=\\s", r8s)
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+    if (length(label_idx) != length(tree_idx)) {
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+        stop("fail to parse the file...")
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+    }
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+
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+    tree_text <- gsub("^tree\\s.*\\s=\\s", "", r8s[tree_idx])
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+    trees <- read.tree(text=tree_text)
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+
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+    label <- gsub("^\\[(\\w+)\\s.*", "\\1", r8s[label_idx])
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+    names(trees) <- label
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+
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+    new("r8s",
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+        file = file,
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+        fields = label,
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+        phylo = trees)
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+}
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+
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+
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+
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+##' @rdname show-methods
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+##' @importFrom ape print.phylo
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+##' @exportMethod show
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+setMethod("show", signature(object = "r8s"),
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+          function(object) {
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+              cat("'r8s' S4 object that stored information of\n\t",
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+                  paste0("'", object@file, "'.\n\n"))
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+              cat("...@ tree: ")
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+              print.phylo(get.tree(object))
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+              ## cat("\nwith the following features available:\n")
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+              ## print_fields(object)
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+          })
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+
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+
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+##' @rdname groupClade-methods
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+##' @exportMethod groupClade
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+##' @param tree which tree selected
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+setMethod("groupClade", signature(object="r8s"),
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+          function(object, node, group_name="group", tree="TREE") {
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+              groupClade_(get.tree(object)[[tree]], node, group_name)
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+          })
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+
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+##' @rdname scale_color-methods
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+##' @exportMethod scale_color
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+##' @param tree which tree selected
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+setMethod("scale_color", signature(object="r8s"),
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+          function(object, by="bootstrap", tree="TREE") {
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+              scale_color_(get.tree(object)[[tree]], by)
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+          })
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+
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+
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+##' @rdname gzoom-methods
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+##' @exportMethod gzoom
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+##' @param tree which tree selected
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+setMethod("gzoom", signature(object="r8s"),
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+          function(object, focus, subtree=FALSE, widths=c(.3, .7), tree="TREE") {
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+              gzoom.phylo(get.tree(object)[[tree]], focus, subtree, widths)
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+          })
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+
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+
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+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+setMethod("get.tree", signature(object="r8s"),
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+          function(object,...) {
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+              object@phylo
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+          }
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+          )
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+
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+
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+##' @rdname get.fields-methods
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+##' @exportMethod get.fields
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+setMethod("get.fields", signature(object="r8s"),
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+          function(object, ...) {
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+              get.fields.tree(object)
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+          }
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+          )
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+