| ... | ... |
@@ -3,9 +3,15 @@ |
| 3 | 3 |
##' |
| 4 | 4 |
##' @title rotate_tree |
| 5 | 5 |
##' @param treeview tree view |
| 6 |
-##' @param angle angle |
|
| 6 |
+##' @param angle the angle of rotation |
|
| 7 | 7 |
##' @return updated tree view |
| 8 | 8 |
##' @export |
| 9 |
+##' @examples |
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| 10 |
+##' tree <- rtree(15) |
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| 11 |
+##' p <- ggtree(tree) + geom_tiplab() |
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| 12 |
+##' p2 <- open_tree(p, 180) |
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| 13 |
+##' p3 <- rotate_tree(p2, 180) |
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| 14 |
+##' p3 |
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| 9 | 15 |
##' @author Guangchuang Yu |
| 10 | 16 |
rotate_tree <- function(treeview, angle) {
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| 11 | 17 |
treeview <- treeview + coord_polar(theta='y', start=(angle-90)/180*pi, -1) |
| ... | ... |
@@ -14,15 +20,19 @@ rotate_tree <- function(treeview, angle) {
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| 14 | 20 |
return(treeview) |
| 15 | 21 |
} |
| 16 | 22 |
|
| 17 |
-##' open tree with specific angle |
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| 23 |
+##' transform a tree in either rectangular or circular layout into the fan layout that opens with a specific angle |
|
| 18 | 24 |
##' |
| 19 | 25 |
##' |
| 20 | 26 |
##' @title open_tree |
| 21 | 27 |
##' @param treeview tree view |
| 22 |
-##' @param angle angle |
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| 28 |
+##' @param angle open the tree at a specific angle |
|
| 23 | 29 |
##' @return updated tree view |
| 24 | 30 |
##' @importFrom ggplot2 scale_y_continuous |
| 25 | 31 |
##' @export |
| 32 |
+##' @examples |
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| 33 |
+##' tree <- rtree(15) |
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| 34 |
+##' p <- ggtree(tree) + geom_tiplab() |
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| 35 |
+##' open_tree(p, 180) |
|
| 26 | 36 |
##' @author Guangchuang Yu |
| 27 | 37 |
open_tree <- function(treeview, angle) {
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| 28 | 38 |
p <- treeview + layout_circular() |
| ... | ... |
@@ -40,24 +50,44 @@ open_tree <- function(treeview, angle) {
|
| 40 | 50 |
return(p) |
| 41 | 51 |
} |
| 42 | 52 |
|
| 53 |
+##' transform circular/fan layout to rectangular layout |
|
| 54 |
+##' |
|
| 55 |
+##' |
|
| 43 | 56 |
##' @title layout_rectangular |
| 44 | 57 |
##' @rdname tree-layout |
| 45 | 58 |
##' @export |
| 59 |
+##' @examples |
|
| 60 |
+##' tree <- rtree(20) |
|
| 61 |
+##' ggtree(tree, layout = "circular") + layout_rectangular() |
|
| 46 | 62 |
layout_rectangular <- function() {
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| 47 | 63 |
layout_ggtree('rectangular')
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| 48 | 64 |
} |
| 49 | 65 |
|
| 66 |
+##' transform rectangular layout to circular layout |
|
| 67 |
+##' |
|
| 68 |
+##' |
|
| 50 | 69 |
##' @title layout_circular |
| 51 | 70 |
##' @rdname tree-layout |
| 52 | 71 |
##' @export |
| 72 |
+##' @examples |
|
| 73 |
+##' tree <- rtree(20) |
|
| 74 |
+##' p <- ggtree(tree) |
|
| 75 |
+##' p + layout_circular() |
|
| 53 | 76 |
layout_circular <- function() {
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| 54 | 77 |
layout_ggtree('circular')
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| 55 | 78 |
} |
| 56 | 79 |
|
| 80 |
+##' transform rectangular/circular layout to inward_circular layout |
|
| 81 |
+##' |
|
| 82 |
+##' |
|
| 57 | 83 |
##' @title layout_inward_circular |
| 58 |
-##' @param xlim x limits |
|
| 84 |
+##' @param xlim setting x limits, which will affect the center space of the tree |
|
| 59 | 85 |
##' @rdname tree-layout |
| 60 | 86 |
##' @export |
| 87 |
+##' @examples |
|
| 88 |
+##' tree <- rtree(20) |
|
| 89 |
+##' p <- ggtree(tree) |
|
| 90 |
+##' p + layout_inward_circular(xlim=4) + geom_tiplab(hjust=1) |
|
| 61 | 91 |
layout_inward_circular <- function(xlim = NULL) {
|
| 62 | 92 |
if (!is.null(xlim) && length(xlim) == 1) {
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| 63 | 93 |
xlim <- c(xlim, 0) |
| ... | ... |
@@ -65,20 +95,31 @@ layout_inward_circular <- function(xlim = NULL) {
|
| 65 | 95 |
layout_ggtree(layout = "inward_circular", xlim = xlim) |
| 66 | 96 |
} |
| 67 | 97 |
|
| 98 |
+##' transform rectangular/circular layout to fan layout |
|
| 99 |
+##' |
|
| 100 |
+##' |
|
| 68 | 101 |
##' @title layout_fan |
| 69 | 102 |
##' @rdname tree-layout |
| 70 | 103 |
##' @param angle open tree at specific angle |
| 71 | 104 |
##' @export |
| 105 |
+##' @examples |
|
| 106 |
+##' tree <- rtree(20) |
|
| 107 |
+##' p <- ggtree(tree) |
|
| 108 |
+##' p + layout_fan(angle=90) |
|
| 72 | 109 |
layout_fan <- function(angle = 180) {
|
| 73 | 110 |
layout_ggtree('fan', angle = angle)
|
| 74 | 111 |
} |
| 75 |
- |
|
| 76 |
-##' tree layout |
|
| 112 |
+ |
|
| 113 |
+##' transform rectangular layout to dendrogram layout |
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| 77 | 114 |
##' |
| 78 | 115 |
##' |
| 79 | 116 |
##' @title layout_dendrogram |
| 80 | 117 |
##' @rdname tree-layout |
| 81 | 118 |
##' @export |
| 119 |
+##' @examples |
|
| 120 |
+##' tree <- rtree(20) |
|
| 121 |
+##' p <- ggtree(tree) |
|
| 122 |
+##' p + p + layout_dendrogram() |
|
| 82 | 123 |
##' @author Guangchuang Yu |
| 83 | 124 |
layout_dendrogram <- function() {
|
| 84 | 125 |
layout_ggtree('dendrogram')
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