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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| calculate.angles.radial <- function(v, tree, spread, total.angle) { | ||
| root.node.id <- v$id[[1]]; | ||
| node.ids <- c(root.node.id); | ||
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|
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| total.angle <- total.angle * spread; | ||
| angles <- numeric(nrow(tree)); | ||
|
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||
| while (length(node.ids) > 0) { | ||
| # "Pops" next element in FIFO queue node.ids | ||
| current.node.id <- node.ids[1]; | ||
| node.ids <- node.ids[-1]; | ||
|
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| parent.id <- tree$parent[tree$tip == current.node.id]; | ||
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| if (parent.id == -1) { | ||
| tree$angle[tree$tip == current.node.id] <- 0; | ||
| } | ||
|
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| child.ids <- tree$tip[tree$parent == current.node.id & !is.na(tree$parent)]; | ||
| num.children <- length(child.ids); | ||
|
|
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| if (num.children > 0) { | ||
| parent.angle <- tree$angle[tree$tip == current.node.id]; | ||
| child.weight <- assign.weight(current.node.id, v); | ||
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| start.angle <- parent.angle - (total.angle) * (num.children > 1) / 2; | ||
| num.slices <- max(num.children - 1, 1); | ||
| angle.increment <- total.angle / num.slices; | ||
|
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||
| for (i in seq_along(child.ids)) { | ||
| child.id <- child.ids[i]; | ||
| angle <- start.angle + (i - 1) * (angle.increment); | ||
| angles[tree$tip == child.id] <- angle; | ||
| } | ||
|
|
||
| # Appending to end of queue for breadth-first traversal | ||
| node.ids <- append(node.ids, child.ids); | ||
| } | ||
| } | ||
|
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| angles <- override.angles(tree, v, angles); | ||
| return(angles); | ||
| } | ||
|
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| calculate.angles.fixed <- function(v, tree, fixed.angle) { | ||
| angles <- numeric(nrow(tree)); | ||
| node.ids <- c(v$id[[1]]); | ||
|
|
||
| while (length(node.ids) > 0) { | ||
| # "Pops" next element in FIFO queue node.ids | ||
| current.node.id <- node.ids[1]; | ||
| node.ids <- node.ids[-1]; | ||
|
|
||
| child.ids <- tree$tip[tree$parent == current.node.id & !is.na(tree$parent)]; | ||
| num.children <- length(child.ids); | ||
| if (num.children > 0) { | ||
| # Safe to hardcode temporarily. This will only ever apply to | ||
| # cases with 0, 1, or 2 children. 3+ will use radial calculation. | ||
|
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||
| # In future, I would like to remove this fixed angle calculation entirely. | ||
| # It would be ideal to handle all calculations in the same way, and | ||
| # rely more on user defined spread and explicit angle overrides. | ||
| child.angles <- if (num.children == 1) c(0) else c(-1, 1) * fixed.angle; | ||
|
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||
| for (i in seq_along(child.ids)) { | ||
| child.id <- child.ids[i]; | ||
| angle <- child.angles[i]; | ||
| angles[tree$tip == child.id] <- angle; | ||
| } | ||
| } | ||
|
|
||
| # Appending to end of queue for breadth-first traversal | ||
| node.ids <- append(node.ids, child.ids); | ||
| } | ||
|
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| angles <- override.angles(tree, v, angles); | ||
| return(angles); | ||
| } | ||
|
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| override.angles <- function(tree, v, angles) { | ||
| if (is.null(v$angle)) { | ||
| v$angle <- NA; | ||
| } | ||
|
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||
| angle.index <- as.list(v$angle); | ||
|
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| names(angle.index) <- v$id; | ||
| angle.index <- angle.index[!is.na(angle.index)]; | ||
|
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| angles <- apply( | ||
| data.frame(tip = tree$tip, angle = angles), | ||
| MARGIN = 1, | ||
| FUN = function(x) { | ||
| node.id <- as.character(x['tip']); | ||
| angle.override <- angle.index[[node.id]]; | ||
| if (!is.null(angle.override)) { | ||
| angle.override <- as.numeric(angle.override); | ||
| } | ||
| angle <- if (is.null(angle.override) || is.na(angle.override)) x['angle'] else angle.override; | ||
| return(as.numeric(angle)); | ||
| } | ||
| ); | ||
|
|
||
| return(angles); | ||
| } |
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