Commit id: 6a8688fb37bcb8dd68977824539842b2e2e1ebe7
remove quote in beast tip/node labels <2015-03-10, Tue>
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@100450 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -1,7 +1,7 @@ |
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Package: ggtree |
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Type: Package |
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Title: a phylogenetic tree viewer for different types of tree annotations |
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-Version: 0.99.21 |
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+Version: 0.99.22 |
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Author: Guangchuang Yu |
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Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
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Description: ggtree extends the ggplot2 plotting system which implemented the |
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@@ -1,3 +1,7 @@ |
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+CHANGES IN VERSION 0.99.22 |
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+------------------------ |
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+ o remove quote in beast tip/node labels <2015-03-10, Tue> |
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+ |
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CHANGES IN VERSION 0.99.21 |
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------------------------ |
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o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue> |
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@@ -15,11 +15,19 @@ read.beast <- function(file) { |
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stats <- read.stats_beast(file) |
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fields <- sub("_lower|_upper", "", names(stats)) %>% unique |
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fields %<>% `[`(.!="node") |
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+ |
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+ phylo <- read.nexus(file) |
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+ if (!is.null(phylo$node.label)) { |
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+ phylo$node.label %<>% gsub("\"*'*", "", .) |
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+ } |
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+ if ( !is.null(phylo$tip.label)) { |
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+ phylo$tip.label %<>% gsub("\"*'*", "", .) |
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+ } |
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new("beast", |
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fields = fields, |
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treetext = read.treetext_beast(file), |
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- phylo = read.nexus(file), |
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+ phylo = phylo, |
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translation = read.trans_beast(file), |
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stats = stats, |
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file = file |
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@@ -124,7 +124,8 @@ fortify.beast <- function(model, data, |
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len <- sapply(stats[,ii], length) |
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if (any(len > 1)) { |
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stats[,ii] %<>% sapply(., function(x) { |
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- y <- unlist(x) %>% as.character %>% gsub("\"", "", .) |
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+ y <- unlist(x) %>% as.character %>% |
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+ gsub("\"", "", .) %>% gsub("'", "", .) |
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if (length(y) == 1) { |
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return(y) |
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} else { |
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@@ -132,7 +133,8 @@ fortify.beast <- function(model, data, |
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} |
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}) |
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} else { |
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- stats[,ii] %<>% unlist %>% as.character %>% gsub("\"", "", .) |
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+ stats[,ii] %<>% unlist %>% as.character %>% |
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+ gsub("\"", "", .) %>% gsub("'", "", .) |
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} |
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next |
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} |