update fortify for pvclust
... | ... |
@@ -32,6 +32,18 @@ scaleY <- function(phylo, df, yscale, layout, ...) { |
32 | 32 |
} |
33 | 33 |
|
34 | 34 |
|
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+adjust_hclust_tip.edge.len <- function(df, phylo){ |
|
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+ mx <- max(df$x, na.rm=TRUE) |
|
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+ df$x <- df$x - mx |
|
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+ df$branch <- df$branch - mx |
|
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+ tip.edge.len <- attr(phylo, 'tip.edge.len') |
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+ if (!is.null(tip.edge.len)){ |
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+ df[df$isTip, "x", drop=TRUE] <- tip.edge.len |
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+ } |
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+ attr(df, 'revts.done') = TRUE |
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+ return(df) |
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+} |
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+ |
|
35 | 47 |
## |
36 | 48 |
## |
37 | 49 |
## old version of fortify.phylo |
... | ... |
@@ -148,14 +148,7 @@ fortify.phylo4 <- function(model, data, |
148 | 148 |
|
149 | 149 |
df <- fortify.phylo(phylo, data, |
150 | 150 |
layout, ladderize, right, mrsd=mrsd, ...) |
151 |
- mx <- max(df$x, na.rm=TRUE) |
|
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- df$x <- df$x - mx |
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- df$branch <- df$branch - mx |
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- tip.edge.len <- attr(phylo, 'tip.edge.len') |
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- if (!is.null(tip.edge.len)){ |
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- df[df$isTip, "x", drop=TRUE] <- tip.edge.len |
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- } |
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- attr(df, 'revts.done') = TRUE |
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+ df <- adjust_hclust_tip.edge.len(df, phylo) |
|
159 | 152 |
scaleY(phylo, df, yscale, layout, ...) |
160 | 153 |
} |
161 | 154 |
|
... | ... |
@@ -205,8 +198,12 @@ fortify.phylo4d <- function(model, data, |
205 | 198 |
right = FALSE, |
206 | 199 |
branch.length = "branch.length", |
207 | 200 |
mrsd = NULL, |
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+ hang = 0.1, |
|
208 | 202 |
...) { |
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- fortify(as.treedata(model), data, layout, yscale, ladderize, right, branch.length, mrsd, ...) |
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+ model <- as.treedata(model, hang = hang) |
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+ df <- fortify(model, data, layout, yscale, ladderize, right, branch.length, mrsd, ...) |
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+ df <- adjust_hclust_tip.edge.len(df, model@phylo) |
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+ return (df) |
|
210 | 207 |
} |
211 | 208 |
|
212 | 209 |
##' @method fortify pvclust |