Browse code

roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
Showing 43 changed files

... ...
@@ -54,3 +54,4 @@ Packaged: 2014-12-03 08:16:14 UTC; root
54 54
 biocViews: Alignment, Annotation, Clustering, DataImport,
55 55
     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
56 56
 RoxygenNote: 6.1.1
57
+Roxygen: list(markdown = TRUE)
... ...
@@ -16,7 +16,7 @@ S3method(fortify,phylog)
16 16
 S3method(fortify,phyloseq)
17 17
 S3method(fortify,treedata)
18 18
 S3method(fortify,twins)
19
-S3method(ggplot_add,align_axis)
19
+S3method(ggplot_add,axisAlign)
20 20
 S3method(ggplot_add,cladelabel)
21 21
 S3method(ggplot_add,facet_plot)
22 22
 S3method(ggplot_add,facet_xlim)
... ...
@@ -45,8 +45,6 @@ export(StatBalance)
45 45
 export(StatHilight)
46 46
 export(add_colorbar)
47 47
 export(aes)
48
-export(align_x)
49
-export(align_y)
50 48
 export(annotation_image)
51 49
 export(arrow)
52 50
 export(as.polytomy)
... ...
@@ -135,8 +133,10 @@ export(theme_tree2)
135 133
 export(unit)
136 134
 export(viewClade)
137 135
 export(xlim)
136
+export(xlim_align)
138 137
 export(xlim_expand)
139 138
 export(xlim_tree)
139
+export(ylim_align)
140 140
 exportMethods(gzoom)
141 141
 exportMethods(scale_color)
142 142
 importFrom(ape,di2multi)
... ...
@@ -1,7 +1,9 @@
1 1
 # ggtree 2.1.1
2 2
 
3
-+ `align_x` and `align_y` for setting x or y limits of a ggplot based on another ggplot object (2019-10-31, Thu)
3
++ convert roxygen documents using markdown (2019-11-01, Fri)
4
++ `xlim_align` and `ylim_align` to uniformize axis limits of ggplot objects (2019-10-31, Thu)
4 5
   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>
6
+  - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>
5 7
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
6 8
   - <https://github.com/YuLab-SMU/ggtree/issues/260>
7 9
 
... ...
@@ -5,7 +5,7 @@ setOldClass("ggtree")
5 5
 ##' @name scale_color
6 6
 ##' @rdname scale_color-methods
7 7
 ##' @title scale_color method
8
-##' @param object \code{treedata} object
8
+##' @param object `treedata` object
9 9
 ##' @param by one of numerical attributes
10 10
 ##' @param ... additional parameter
11 11
 ##' @return color vector
... ...
@@ -58,29 +58,51 @@ revts <- function(treeview) {
58 58
 
59 59
 
60 60
 
61
-##' set axis limits (x or y specific by 'by' parameter) of a ggplot object (left hand side)
62
-##' based on the x (align_x function) or y (align_y function) limits of another ggplot object (right hand side).
63
-##' This is useful for using cowplot or patchwork to align ggplot objects.
61
+##' set axis limits (x or y) of a `ggplot` object (left hand side of `+`)
62
+##' based on the x (`xlim_align`) or y (`ylim_align`) limits of another `ggplot` object (right hand side of `+`).
63
+##' This is useful for using `cowplot` or `patchwork` to align `ggplot` objects.
64 64
 ##'
65 65
 ##'
66
-##' @title align_x
66
+##' @title xlim_align
67 67
 ##' @rdname align_axis
68 68
 ##' @param gg ggplot object
69
-##' @param expand_limits amount to expand the limits
70
-##' @param by one of 'x' or 'y'
71
-##' @return ggplot2 object with new limits and expand
72
-##' @importFrom ggplot2 expand_scale
69
+##' @param limits vector of limits. If NULL, determine from `gg`. 
70
+##' @return ggplot2 object with new limits
73 71
 ##' @export
74 72
 ##' @author Guangchuang Yu
75
-align_x <- function(gg, expand_limits = expand_scale(0, 0.6), by = 'x') {
76
-    structure(list(gg = gg, expand_limits = expand_limits, by = by, axis = "x"),
77
-              class = "align_axis")
73
+xlim_align <- function(gg, limits = NULL) {
74
+    axis_align(gg = gg, limits = limits, axis = 'x')
78 75
 }
79 76
 
80 77
 ##' @rdname align_axis
81
-##' @title align_y
78
+##' @title ylim_align
82 79
 ##' @export
83
-align_y <- function(gg, expand_limits = expand_scale(0, 0.6), by = 'y') { 
84
-    structure(list(gg = gg, expand_limits = expand_limits, by = by, axis = "y"),
85
-              class = "align_axis")
80
+ylim_align <- function(gg, limits = NULL) {
81
+    axis_align(gg = gg, limits = limits, axis = 'y')
86 82
 }
83
+
84
+axis_align <- function(gg, limits = NULL, axis) {
85
+    if (is.null(limits)) {
86
+        if (axis == "x") {
87
+            limits <- xrange(gg)
88
+        } else {
89
+            limits <- yrange(gg)
90
+        }
91
+    }
92
+    structure(list(limits = limits, axis = axis),
93
+              class = "axisAlign")
94
+}
95
+
96
+
97
+yrange <- function(gg) {
98
+    ggrange(gg, "y.range")
99
+}
100
+
101
+xrange <- function(gg) {
102
+    ggrange(gg, "x.range")
103
+}
104
+
105
+ggrange <- function(gg, var) {
106
+    ggplot_build(gg)$layout$panel_params[[1]][[var]]
107
+}
108
+
... ...
@@ -42,7 +42,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {
42 42
     ## xd <- tree_view$data$branch.length[node]/2
43 43
 
44 44
     cpos <- get_clade_position(tree_view, node=node)
45
-    xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2]
45
+    xmax <- xrange(tree_view)[2]
46 46
 
47 47
     attr(tree_view, 'viewClade') <- TRUE
48 48
     attr(tree_view, 'viewClade_node') <- node
... ...
@@ -51,8 +51,8 @@ phylopic <- function(tree_view, phylopic_id,
51 51
 ##' @param subview a ggplot or grob object
52 52
 ##' @param x x position
53 53
 ##' @param y y position
54
-##' @param width width of subview, [0,1]
55
-##' @param height height of subview, [0,1]
54
+##' @param width width of subview
55
+##' @param height height of subview
56 56
 ##' @return ggplot object
57 57
 ##' @importFrom ggplot2 annotation_custom
58 58
 ##' @importFrom ggplot2 ggplotGrob
... ...
@@ -122,7 +122,7 @@ gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
122 122
 ##' @title gzoom method
123 123
 ##' @rdname gzoom-methods
124 124
 ##' @exportMethod gzoom
125
-##' @param xmax_adjust adjust xmax (xlim[2])
125
+##' @param xmax_adjust adjust xmax (`xlim[2]`)
126 126
 ##' @aliases gzoom,ggtree-method
127 127
 setMethod("gzoom", signature(object="ggtree"),
128 128
           function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
... ...
@@ -4,7 +4,7 @@
4 4
 ##' @title range_format
5 5
 ##' @param x input list
6 6
 ##' @param trans transformation function
7
-##' @return character vector of '[lower, upper]'
7
+##' @return character vector of `[lower, upper]`
8 8
 ##' @export
9 9
 ##' @author Guangchuang Yu
10 10
 range_format <- function(x, trans = NULL) {
... ...
@@ -16,8 +16,8 @@
16 16
 #' @importFrom ggplot2 GeomRect
17 17
 #' @importFrom utils packageVersion
18 18
 #' @author Justin Silverman and modified by Guangchuang Yu
19
-#' @references J. Silverman, et al. \emph{A phylogenetic transform enhances
20
-#'   analysis of compositional microbiota data}. (in preparation)
19
+#' @references J. Silverman, et al. *A phylogenetic transform enhances
20
+#'   analysis of compositional microbiota data*. (in preparation)
21 21
 geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend=0, extendto=NULL) {
22 22
 
23 23
   data = NULL
... ...
@@ -21,7 +21,7 @@
21 21
 ##' @return ggplot layers
22 22
 ##' @export
23 23
 ##' @author Guangchuang Yu
24
-##' @seealso \link{geom_cladelabel2}
24
+##' @seealso [geom_cladelabel2]
25 25
 geom_cladelabel <- function(node, label,
26 26
                             offset      = 0,
27 27
                             offset.text = 0,
... ...
@@ -7,7 +7,7 @@
7 7
 ##' @return ggplot layers
8 8
 ##' @export
9 9
 ##' @author JustGitting
10
-##' @seealso \link{geom_cladelabel}
10
+##' @seealso [geom_cladelabel]
11 11
 geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,
12 12
                             align=FALSE, barsize=0.5, fontsize=3.88, hjust = 0,
13 13
                             geom="text",
... ...
@@ -23,7 +23,7 @@
23 23
 ##' @importFrom ggplot2 position_nudge
24 24
 ##' @export
25 25
 ##' @seealso
26
-##' \link[ggplot2]{geom_label}
26
+##' [geom_label][ggplot2::geom_label]
27 27
 ##' @author Guangchuang Yu
28 28
 geom_label2 <- function(mapping = NULL, data = NULL,
29 29
                         ...,
... ...
@@ -105,7 +105,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,
105 105
 ##' @importFrom ggplot2 layer
106 106
 ##' @export
107 107
 ##' @seealso
108
-##' \link[ggplot2]{geom_point}
108
+##' [geom_point][ggplot2::geom_point]
109 109
 ##' @return point layer
110 110
 ##' @author Guangchuang Yu
111 111
 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",
... ...
@@ -42,7 +42,7 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {
42 42
 ##' @importFrom ggplot2 layer
43 43
 ##' @export
44 44
 ##' @seealso
45
-##' \link[ggplot2]{geom_segment}
45
+##' [geom_segment][ggplot2::geom_segment]
46 46
 ##' @return add segment layer
47 47
 ##' @author Guangchuang Yu
48 48
 geom_segment2 <- function(mapping = NULL, data = NULL, stat = "identity",
... ...
@@ -23,7 +23,7 @@
23 23
 ##' @importFrom rvcheck get_aes_var
24 24
 ##' @export
25 25
 ##' @seealso
26
-##' \link[ggplot2]{geom_text}
26
+##' [geom_text][ggplot2::geom_text]
27 27
 ##' @author Guangchuang Yu
28 28
 geom_text2 <- function(mapping = NULL, data = NULL,
29 29
                        ...,
... ...
@@ -95,8 +95,8 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, lin
95 95
 ##' @return tip label layer
96 96
 ##' @export
97 97
 ##' @author Guangchuang Yu
98
-##' @references \url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
99
-##' @seealso \link{geom_tiplab}
98
+##' @references <https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0>
99
+##' @seealso [geom_tiplab]
100 100
 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {
101 101
     angle <- isTip <- node <- NULL
102 102
     m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle, node = node)
... ...
@@ -1,5 +1,5 @@
1 1
 ##' visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
2
-##' \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.
2
+##' `ggtree` provides functions for visualizing phylogenetic tree and its associated data in R.
3 3
 ##'
4 4
 ##' If you use ggtree in published research, please cite:
5 5
 ##' Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
... ...
@@ -9,10 +9,10 @@
9 9
 ##' @param as.Date logical whether using Date class in time tree
10 10
 ##' @param yscale y scale
11 11
 ##' @param yscale_mapping yscale mapping for category variable
12
-##' @param ladderize logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'
12
+##' @param ladderize logical (default `TRUE`). Should the tree be re-organized to have a 'ladder'
13 13
 ##' aspect?
14
-##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
15
-##' right-hand side? See \code{\link[ape]{ladderize}} for more information. 
14
+##' @param right logical. If `ladderize = TRUE`, should the ladder have the smallest clade on the
15
+##' right-hand side? See [ape::ladderize()] for more information. 
16 16
 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram
17 17
 ##' @param root.position position of the root node (default = 0)
18 18
 ##' @return tree
... ...
@@ -26,7 +26,7 @@
26 26
 ##' @importFrom ggplot2 coord_polar
27 27
 ##' @export
28 28
 ##' @author Yu Guangchuang
29
-##' @seealso \code{\link[ape]{ladderize}}
29
+##' @seealso [ape::ladderize()]
30 30
 ##' @examples
31 31
 ##' require(ape)
32 32
 ##' tr <- rtree(10)
... ...
@@ -21,49 +21,46 @@ ggplot_add.facet_xlim <- function(object, plot, object_name) {
21 21
 }
22 22
 
23 23
 
24
-##' @method ggplot_add align_axis
24
+##' @method ggplot_add axisAlign
25 25
 ##' @export
26
-ggplot_add.align_axis <- function(object, plot, object_name) {
27
-    gg <- object$gg
28
-    v <- get_aes_var(gg$mapping, object$axis)
29
-    limits <- range(gg$data[[v]])
30
-
31
-    expand_limits <- object$expand_limits
32
-    limits[1] <- limits[1] + (limits[1] * expand_limits[1]) - expand_limits[2]
33
-    limits[2] <- limits[2] + (limits[2] * expand_limits[3]) + expand_limits[4]
26
+ggplot_add.axisAlign <- function(object, plot, object_name) {
27
+    limits <- object$limits
28
+    ## expand_limits <- object$expand_limits
29
+    ## limits[1] <- limits[1] + (limits[1] * expand_limits[1]) - expand_limits[2]
30
+    ## limits[2] <- limits[2] + (limits[2] * expand_limits[3]) + expand_limits[4]
34 31
 
35 32
     if (object$axis == 'x') {
36
-        if (object$by == "x") {
37
-            if (is(plot$coordinates, "CoordFlip")) {
38
-                message("the plot was flipped and the x limits will be applied to y-axis")
39
-                scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))
40
-            } else {
41
-                scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))
42
-            }
33
+        ## if (object$by == "x") {
34
+        if (is(plot$coordinates, "CoordFlip")) {
35
+            message("the plot was flipped and the x limits will be applied to y-axis")
36
+            scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))
43 37
         } else {
44
-            if (is(plot$coordinates, "CoordFlip")) {
45
-                message("the plot was flipped and the x limits will be applied to x-axis")
46
-                scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))
47
-            } else {
48
-                scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))
49
-            }
38
+            scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))
50 39
         }
40
+        ## } else {
41
+        ##     if (is(plot$coordinates, "CoordFlip")) {
42
+        ##         message("the plot was flipped and the x limits will be applied to x-axis")
43
+        ##         scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))
44
+        ##     } else {
45
+        ##         scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))
46
+        ##     }
47
+        ## }
51 48
     } else { ## axis == 'y'
52
-        if (object$by == "x") {
53
-            if (is(plot$coordinates, "CoordFlip")) {
54
-                message("the plot was flipped and the y limits will be applied to y-axis")
55
-                scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))
56
-            } else {
57
-                scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))
58
-            }
49
+        ## if (object$by == "x") {
50
+        ##     if (is(plot$coordinates, "CoordFlip")) {
51
+        ##         message("the plot was flipped and the y limits will be applied to y-axis")
52
+        ##         scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))
53
+        ##     } else {
54
+        ##         scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))
55
+        ##     }
56
+        ## } else {
57
+        if (is(plot$coordinates, "CoordFlip")) {
58
+            message("the plot was flipped and the y limits will be applied to x-axis")
59
+            scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))
59 60
         } else {
60
-            if (is(plot$coordinates, "CoordFlip")) {
61
-                message("the plot was flipped and the y limits will be applied to x-axis")
62
-                scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))
63
-            } else {
64
-                scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))
65
-            }
61
+            scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))
66 62
         }
63
+        ## }
67 64
     }
68 65
     ggplot_add(scale_lim, plot, object_name)
69 66
 }
... ...
@@ -78,6 +75,7 @@ ggplot_add.geom_range <- function(object, plot, object_name) {
78 75
 }
79 76
 
80 77
 ##' @method ggplot_add layout_ggtree
78
+##' @importFrom ggplot2 expand_scale
81 79
 ##' @export
82 80
 ggplot_add.layout_ggtree <- function(object, plot, object_name) {
83 81
     if(object$layout == 'fan') {
... ...
@@ -290,13 +290,13 @@ applyLayoutDaylight <- function(df, node_id){
290 290
 
291 291
 
292 292
 ##' Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and
293
-##' left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in [0, 2] (0 to 360) domain.
293
+##' left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in `[0, 2]` (0 to 360) domain.
294 294
 ##'
295 295
 ##' @title getTreeArcAngles
296 296
 ##' @param df tree data.frame
297 297
 ##' @param origin_id node id from which to calculate left and right hand angles of subtree.
298 298
 ##' @param subtree named list of root id of subtree (node) and list of node ids for given subtree (subtree).
299
-##' @return named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.
299
+##' @return named list with right and left angles in range `[0,2]` i.e 1 = 180 degrees, 1.5 = 270 degrees.
300 300
 getTreeArcAngles <- function(df, origin_id, subtree) {
301 301
     df_x = df$x
302 302
     df_y = df$y
... ...
@@ -437,11 +437,12 @@ getTreeArcAngles <- function(df, origin_id, subtree) {
437 437
 
438 438
 ##' Rotate the points in a tree data.frame around a pivot node by the angle specified.
439 439
 ##'
440
-##' @title rotateTreePoints.data.fram
440
+##' @title rotateTreePoints.data.frame
441
+##' @rdname rotateTreePoints
441 442
 ##' @param df tree data.frame
442 443
 ##' @param pivot_node is the id of the pivot node.
443 444
 ##' @param nodes list of node numbers that are to be rotated by angle around the pivot_node
444
-##' @param angle in range [0,2], ie degrees/180, radians/pi
445
+##' @param angle in range `[0,2]`, ie degrees/180, radians/pi
445 446
 ##' @return updated tree data.frame with points rotated by angle
446 447
 rotateTreePoints.df <- function(df, pivot_node, nodes, angle){
447 448
   # Rotate nodes around pivot_node.
... ...
@@ -477,7 +478,7 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){
477 478
 ##' @param df tree data.frame
478 479
 ##' @param origin_node_id origin node id number
479 480
 ##' @param node_id end node id number
480
-##' @return angle in range [-1, 1], i.e. degrees/180, radians/pi
481
+##' @return angle in range `[-1, 1]`, i.e. degrees/180, radians/pi
481 482
 getNodeAngle.df <- function(df, origin_node_id, node_id){
482 483
   if (origin_node_id != node_id) {
483 484
     df_x = df$x
... ...
@@ -1,6 +1,5 @@
1 1
 
2 2
 
3
-
4 3
 ##' @importFrom ggplot2 last_plot
5 4
 get_tree_view <- function(tree_view) {
6 5
     if (is.null(tree_view))
... ...
@@ -1,28 +1,26 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/x-axis.R
3
-\name{align_x}
4
-\alias{align_x}
5
-\alias{align_y}
6
-\title{align_x}
2
+% Please edit documentation in R/axis.R
3
+\name{xlim_align}
4
+\alias{xlim_align}
5
+\alias{ylim_align}
6
+\title{xlim_align}
7 7
 \usage{
8
-align_x(gg, expand_limits = expand_scale(0, 0.6), by = "x")
8
+xlim_align(gg, limits = NULL)
9 9
 
10
-align_y(gg, expand_limits = expand_scale(0, 0.6), by = "y")
10
+ylim_align(gg, limits = NULL)
11 11
 }
12 12
 \arguments{
13 13
 \item{gg}{ggplot object}
14 14
 
15
-\item{expand_limits}{amount to expand the limits}
16
-
17
-\item{by}{one of 'x' or 'y'}
15
+\item{limits}{vector of limits. If NULL, determine from \code{gg}.}
18 16
 }
19 17
 \value{
20
-ggplot2 object with new limits and expand
18
+ggplot2 object with new limits
21 19
 }
22 20
 \description{
23
-set axis limits (x or y specific by 'by' parameter) of a ggplot object (left hand side)
24
-based on the x (align_x function) or y (align_y function) limits of another ggplot object (right hand side).
25
-This is useful for using cowplot or patchwork to align ggplot objects.
21
+set axis limits (x or y) of a \code{ggplot} object (left hand side of \code{+})
22
+based on the x (\code{xlim_align}) or y (\code{ylim_align}) limits of another \code{ggplot} object (right hand side of \code{+}).
23
+This is useful for using \code{cowplot} or \code{patchwork} to align \code{ggplot} objects.
26 24
 }
27 25
 \author{
28 26
 Guangchuang Yu
... ...
@@ -15,7 +15,7 @@ facet_data(tree_view, panel)
15 15
 data frame or a list of data frames
16 16
 }
17 17
 \description{
18
-extract data used in `facet_plot` or `geom_facet`
18
+extract data used in \code{facet_plot} or \code{geom_facet}
19 19
 }
20 20
 \author{
21 21
 Guangchuang Yu
... ...
@@ -32,7 +32,7 @@ correspond to multichotomies will not be displayed.
32 32
 }
33 33
 \references{
34 34
 J. Silverman, et al. \emph{A phylogenetic transform enhances
35
-  analysis of compositional microbiota data}. (in preparation)
35
+analysis of compositional microbiota data}. (in preparation)
36 36
 }
37 37
 \author{
38 38
 Justin Silverman and modified by Guangchuang Yu
... ...
@@ -49,7 +49,7 @@ label layer
49 49
 geom_label2 support aes(subset) via setup_data
50 50
 }
51 51
 \seealso{
52
-\link[ggplot2]{geom_label}
52
+\link[ggplot2:geom_label]{geom_label}
53 53
 }
54 54
 \author{
55 55
 Guangchuang Yu
... ...
@@ -11,7 +11,7 @@ geom_motif(mapping, data, on, label, align = "centre", ...)
11 11
 
12 12
 \item{data}{data}
13 13
 
14
-\item{on}{gene to center (i.e. set middle position of the `on` gene to 0)}
14
+\item{on}{gene to center (i.e. set middle position of the \code{on} gene to 0)}
15 15
 
16 16
 \item{label}{specify a column to be used to label genes}
17 17
 
... ...
@@ -32,7 +32,7 @@ point layer
32 32
 geom_point2 support aes(subset) via setup_data
33 33
 }
34 34
 \seealso{
35
-\link[ggplot2]{geom_point}
35
+\link[ggplot2:geom_point]{geom_point}
36 36
 }
37 37
 \author{
38 38
 Guangchuang Yu
... ...
@@ -30,7 +30,7 @@ geom_segment2(mapping = NULL, data = NULL, stat = "identity",
30 30
 
31 31
 \item{arrow}{specification for arrow heads, as created by arrow().}
32 32
 
33
-\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}
33
+\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}
34 34
 
35 35
 \item{...}{additional parameter}
36 36
 }
... ...
@@ -41,7 +41,7 @@ add segment layer
41 41
 geom_segment2 support aes(subset) via setup_data
42 42
 }
43 43
 \seealso{
44
-\link[ggplot2]{geom_segment}
44
+\link[ggplot2:geom_segment]{geom_segment}
45 45
 }
46 46
 \author{
47 47
 Guangchuang Yu
... ...
@@ -18,7 +18,7 @@ positive values produce right-hand curves, and zero produces a straight line.}
18 18
 
19 19
 \item{arrow}{specification for arrow heads, as created by arrow().}
20 20
 
21
-\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}
21
+\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}
22 22
 
23 23
 \item{...}{additional parameter}
24 24
 }
... ...
@@ -44,7 +44,7 @@ text layer
44 44
 geom_text2 support aes(subset) via setup_data
45 45
 }
46 46
 \seealso{
47
-\link[ggplot2]{geom_text}
47
+\link[ggplot2:geom_text]{geom_text}
48 48
 }
49 49
 \author{
50 50
 Guangchuang Yu
... ...
@@ -14,7 +14,7 @@ getNodeAngle.df(df, origin_node_id, node_id)
14 14
 \item{node_id}{end node id number}
15 15
 }
16 16
 \value{
17
-angle in range [-1, 1], i.e. degrees/180, radians/pi
17
+angle in range \code{[-1, 1]}, i.e. degrees/180, radians/pi
18 18
 }
19 19
 \description{
20 20
 Get the angle between the two nodes specified.
... ...
@@ -14,9 +14,9 @@ getTreeArcAngles(df, origin_id, subtree)
14 14
 \item{subtree}{named list of root id of subtree (node) and list of node ids for given subtree (subtree).}
15 15
 }
16 16
 \value{
17
-named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.
17
+named list with right and left angles in range \code{[0,2]} i.e 1 = 180 degrees, 1.5 = 270 degrees.
18 18
 }
19 19
 \description{
20 20
 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and
21
-left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in [0, 2] (0 to 360) domain.
21
+left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in \code{[0, 2]} (0 to 360) domain.
22 22
 }
... ...
@@ -7,7 +7,7 @@
7 7
 get_heatmap_column_position(treeview, by = "bottom")
8 8
 }
9 9
 \arguments{
10
-\item{treeview}{output of `gheatmap`}
10
+\item{treeview}{output of \code{gheatmap}}
11 11
 
12 12
 \item{by}{one of 'bottom' or 'top'}
13 13
 }
... ...
@@ -16,7 +16,7 @@ data.frame
16 16
 }
17 17
 \description{
18 18
 return a data.frame that contains position information
19
-for labeling column names of heatmap produced by `gheatmap` function
19
+for labeling column names of heatmap produced by \code{gheatmap} function
20 20
 }
21 21
 \author{
22 22
 Guangchuang Yu
... ...
@@ -34,7 +34,7 @@ ggtree(tr, mapping = NULL, layout = "rectangular", open.angle = 0,
34 34
 aspect?}
35 35
 
36 36
 \item{right}{logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
37
-right-hand side? See \code{\link[ape]{ladderize}} for more information.}
37
+right-hand side? See \code{\link[ape:ladderize]{ape::ladderize()}} for more information.}
38 38
 
39 39
 \item{branch.length}{variable for scaling branch, if 'none' draw cladogram}
40 40
 
... ...
@@ -59,7 +59,7 @@ tr <- rtree(10)
59 59
 ggtree(tr)
60 60
 }
61 61
 \seealso{
62
-\code{\link[ape]{ladderize}}
62
+\code{\link[ape:ladderize]{ape::ladderize()}}
63 63
 }
64 64
 \author{
65 65
 Yu Guangchuang
... ...
@@ -30,7 +30,7 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
30 30
 
31 31
 \item{...}{additional parameter}
32 32
 
33
-\item{xmax_adjust}{adjust xmax (xlim[2])}
33
+\item{xmax_adjust}{adjust xmax (\code{xlim[2]})}
34 34
 }
35 35
 \value{
36 36
 figure
... ...
@@ -21,15 +21,12 @@ tree as data.frame with equal angle layout.
21 21
 }
22 22
 \references{
23 23
 The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"
24
-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.
25
-
26
-```
27
-Leafs are subtrees with no children
24
+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children
28 25
 Initialise tree using equal angle algorithm
29 26
 tree_df = equal_angle(tree)
30 27
 
31 28
 nodes = get list of nodes in tree_df breadth-first
32 29
 nodes = remove tip nodes.
33 30
 
34
-```
31
+}
35 32
 }
... ...
@@ -12,7 +12,7 @@ range_format(x, trans = NULL)
12 12
 \item{trans}{transformation function}
13 13
 }
14 14
 \value{
15
-character vector of '[lower, upper]'
15
+character vector of \code{[lower, upper]}
16 16
 }
17 17
 \description{
18 18
 format a list of range (HPD, CI, etc that has length of 2)
... ...
@@ -1,5 +1,5 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/x-axis.R
2
+% Please edit documentation in R/axis.R
3 3
 \name{revts}
4 4
 \alias{revts}
5 5
 \title{revts}
6 6
similarity index 84%
7 7
rename from man/rotateTreePoints.df.Rd
8 8
rename to man/rotateTreePoints.Rd
... ...
@@ -2,7 +2,7 @@
2 2
 % Please edit documentation in R/tree-utilities.R
3 3
 \name{rotateTreePoints.df}
4 4
 \alias{rotateTreePoints.df}
5
-\title{rotateTreePoints.data.fram}
5
+\title{rotateTreePoints.data.frame}
6 6
 \usage{
7 7
 rotateTreePoints.df(df, pivot_node, nodes, angle)
8 8
 }
... ...
@@ -13,7 +13,7 @@ rotateTreePoints.df(df, pivot_node, nodes, angle)
13 13
 
14 14
 \item{nodes}{list of node numbers that are to be rotated by angle around the pivot_node}
15 15
 
16
-\item{angle}{in range [0,2], ie degrees/180, radians/pi}
16
+\item{angle}{in range \code{[0,2]}, ie degrees/180, radians/pi}
17 17
 }
18 18
 \value{
19 19
 updated tree data.frame with points rotated by angle
... ...
@@ -1,5 +1,5 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/x-axis.R
2
+% Please edit documentation in R/axis.R
3 3
 \name{scale_x_range}
4 4
 \alias{scale_x_range}
5 5
 \title{scale_x_range}
... ...
@@ -15,9 +15,9 @@ subview(mainview, subview, x, y, width = 0.1, height = 0.1)
15 15
 
16 16
 \item{y}{y position}
17 17
 
18
-\item{width}{width of subview, [0,1]}
18
+\item{width}{width of subview}
19 19
 
20
-\item{height}{height of subview, [0,1]}
20
+\item{height}{height of subview}
21 21
 }
22 22
 \value{
23 23
 ggplot object
... ...
@@ -1,5 +1,5 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/x-axis.R
2
+% Please edit documentation in R/axis.R
3 3
 \name{xlim_expand}
4 4
 \alias{xlim_expand}
5 5
 \title{xlim_expand}
... ...
@@ -1,5 +1,5 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/x-axis.R
2
+% Please edit documentation in R/axis.R
3 3
 \name{xlim_tree}
4 4
 \alias{xlim_tree}
5 5
 \title{xlim_tree}