git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117269 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: 1.5.1 |
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+Version: 1.5.2 |
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Author: Guangchuang Yu and Tommy Tsan-Yuk Lam |
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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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@@ -44,15 +44,17 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color= |
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start <- max(df$x) + offset |
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|
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dd <- data |
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- dd$lab <- rownames(dd) |
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- dd <- dd[df$label[order(df$y)],] |
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+ ## dd$lab <- rownames(dd) |
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+ lab <- df$label[order(df$y)] |
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+ dd <- dd[lab, ] |
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dd$y <- sort(df$y) |
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- |
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+ dd$lab <- lab |
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## dd <- melt(dd, id=c("lab", "y")) |
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dd <- gather(dd, variable, value, -c(lab, y)) |
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- |
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- if (any(dd$value == "")) { |
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- dd$value[dd$value == ""] <- NA |
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+ |
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+ i <- which(dd$value == "") |
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+ if (length(i) > 0) { |
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+ dd$value[i] <- NA |
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} |
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if (is.null(colnames_level)) { |
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dd$variable <- factor(dd$variable, levels=colnames(data)) |
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@@ -87,7 +89,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color= |
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} |
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|
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p2 <- p2 + theme(legend.position="right", legend.title=element_blank()) |
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- p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL))) |
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+ ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL))) |
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|
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attr(p2, "mapping") <- mapping |
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return(p2) |
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@@ -412,6 +412,15 @@ fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none", |
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scaleY(phylo, df, yscale, layout, ...) |
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} |
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+##' @method fortify phylo4d |
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+##' @export |
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+fortify.phylo4d <- function(model, data, layout="rectangular", yscale="none", |
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+ ladderize=TRUE, right=FALSE, mrsd=NULL, ...) { |
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+ res <- fortify.phylo4(model, data, layout, yscale, ladderize, right, mrsd, ...) |
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+ tdata <- model@data[match(res$node, rownames(model@data)), , drop=FALSE] |
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+ cbind(res, tdata) |
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+} |
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+ |
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as.phylo.phylo4 <- function(phylo4) { |
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edge <- phylo4@edge |
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edge <- edge[edge[,1] != 0, ] |