... | ... |
@@ -10,6 +10,7 @@ S3method(fortify,phylo4d) |
10 | 10 |
S3method(fortify,phyloseq) |
11 | 11 |
S3method(fortify,treedata) |
12 | 12 |
S3method(ggplot_add,facet_xlim) |
13 |
+S3method(ggplot_add,scale_ggtree) |
|
13 | 14 |
S3method(groupClade,ggtree) |
14 | 15 |
S3method(groupOTU,ggtree) |
15 | 16 |
S3method(identify,gg) |
... | ... |
@@ -186,6 +187,7 @@ importFrom(ggplot2,scale_x_reverse) |
186 | 187 |
importFrom(ggplot2,scale_y_continuous) |
187 | 188 |
importFrom(ggplot2,theme) |
188 | 189 |
importFrom(ggplot2,theme_bw) |
190 |
+importFrom(ggplot2,waiver) |
|
189 | 191 |
importFrom(ggplot2,xlab) |
190 | 192 |
importFrom(ggplot2,xlim) |
191 | 193 |
importFrom(ggplot2,ylab) |
... | ... |
@@ -1,5 +1,6 @@ |
1 | 1 |
# ggtree 1.17.1 |
2 | 2 |
|
3 |
++ update `scale_x_ggtree`, now we can use `gheatmap() + scale_x_ggtree()` (2019-05-22, Wed) |
|
3 | 4 |
+ extend `xlim_expand` to work with `ggplot2` (2019-05-20, Tue) |
4 | 5 |
- <https://yulab-smu.github.io/treedata-book/chapter9.html#xlim_expand> |
5 | 6 |
+ add `legend_title` variable in `gheatmap` (2019-05-16, Thu) |
... | ... |
@@ -84,58 +84,6 @@ get_heatmap_column_position <- function(treeview, by="bottom") { |
84 | 84 |
return(mapping) |
85 | 85 |
} |
86 | 86 |
|
87 |
-##' scale x for tree with heatmap |
|
88 |
-##' |
|
89 |
-##' |
|
90 |
-##' @title scale_x_ggtree |
|
91 |
-##' @param tree_view tree view |
|
92 |
-##' @param breaks breaks for tree |
|
93 |
-##' @param labels lables for corresponding breaks |
|
94 |
-##' @return tree view |
|
95 |
-##' @importFrom ggplot2 scale_x_continuous |
|
96 |
-##' @importFrom ggplot2 scale_x_date |
|
97 |
-##' @export |
|
98 |
-##' @author Guangchuang Yu |
|
99 |
-scale_x_ggtree <- function(tree_view, breaks=NULL, labels=NULL) { |
|
100 |
- p <- get_tree_view(tree_view) |
|
101 |
- |
|
102 |
- mrsd <- get("mrsd", envir=tree_view$plot_env) |
|
103 |
- if (!is.null(mrsd) && class(p$data$x) == "Date") { |
|
104 |
- x <- Date2decimal(p$data$x) |
|
105 |
- } else { |
|
106 |
- x <- p$data$x |
|
107 |
- } |
|
108 |
- |
|
109 |
- if (is.null(breaks)) { |
|
110 |
- breaks <- graphics::hist(x, breaks=5, plot=FALSE)$breaks |
|
111 |
- } |
|
112 |
- m <- attr(p, "mapping") |
|
113 |
- |
|
114 |
- if (!is.null(mrsd) &&class(m$to) == "Date") { |
|
115 |
- to <- Date2decimal(m$to) |
|
116 |
- } else { |
|
117 |
- to <- m$to |
|
118 |
- } |
|
119 |
- |
|
120 |
- idx <- which(sapply(breaks, function(x) any(x > m$to))) |
|
121 |
- if (length(idx)) { |
|
122 |
- breaks <- breaks[-idx] |
|
123 |
- } |
|
124 |
- |
|
125 |
- if (is.null(labels)) { |
|
126 |
- labels <- breaks |
|
127 |
- } |
|
128 |
- |
|
129 |
- breaks <- c(breaks, to) |
|
130 |
- labels <- c(labels, gsub("\\.", "", as.character(m$from))) |
|
131 |
- |
|
132 |
- if (!is.null(mrsd) && class(p$data$x) == "Date") { |
|
133 |
- p <- p + scale_x_date(breaks=decimal2Date(breaks), labels) |
|
134 |
- } else { |
|
135 |
- p <- p + scale_x_continuous(breaks=breaks, labels=labels) |
|
136 |
- } |
|
137 |
- return(p) |
|
138 |
-} |
|
139 | 87 |
|
140 | 88 |
|
141 | 89 |
|
142 | 90 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,64 @@ |
1 |
+##' scale x for tree with gheatmap |
|
2 |
+##' |
|
3 |
+##' |
|
4 |
+##' @title scale_x_ggtree |
|
5 |
+##' @param breaks breaks for tree |
|
6 |
+##' @param labels lables for corresponding breaks |
|
7 |
+##' @return updated tree view |
|
8 |
+##' @importFrom ggplot2 waiver |
|
9 |
+##' @export |
|
10 |
+##' @author Guangchuang Yu |
|
11 |
+scale_x_ggtree <- function(breaks = waiver(), labels = waiver()) { |
|
12 |
+ structure(list(breaks = breaks, labels = labels), class="scale_ggtree") |
|
13 |
+} |
|
14 |
+ |
|
15 |
+ |
|
16 |
+##' @importFrom ggplot2 scale_x_continuous |
|
17 |
+##' @importFrom ggplot2 scale_x_date |
|
18 |
+##' @method ggplot_add scale_ggtree |
|
19 |
+##' @export |
|
20 |
+ggplot_add.scale_ggtree <- function(object, plot, object_name) { |
|
21 |
+ mrsd <- get("mrsd", envir = plot$plot_env) |
|
22 |
+ if (!is.null(mrsd) && class(plot$data$x) == "Date") { |
|
23 |
+ x <- Date2decimal(plot$data$x) |
|
24 |
+ } else { |
|
25 |
+ x <- plot$data$x |
|
26 |
+ } |
|
27 |
+ |
|
28 |
+ breaks <- object$breaks |
|
29 |
+ labels <- object$labels |
|
30 |
+ |
|
31 |
+ if (length(breaks) == 0) { |
|
32 |
+ breaks <- graphics::hist(x, breaks=5, plot=FALSE)$breaks |
|
33 |
+ } |
|
34 |
+ m <- attr(plot, "mapping") |
|
35 |
+ |
|
36 |
+ if (!is.null(mrsd) && class(m$to) == "Date") { |
|
37 |
+ to <- Date2decimal(m$to) |
|
38 |
+ } else { |
|
39 |
+ to <- m$to |
|
40 |
+ } |
|
41 |
+ |
|
42 |
+ idx <- which(sapply(breaks, function(x) any(x > m$to))) |
|
43 |
+ if (length(idx)) { |
|
44 |
+ breaks <- breaks[-idx] |
|
45 |
+ } |
|
46 |
+ |
|
47 |
+ if (length(labels) == 0) { |
|
48 |
+ labels <- breaks |
|
49 |
+ } |
|
50 |
+ |
|
51 |
+ if (length(breaks) != length(labels)) { |
|
52 |
+ stop("breaks and labels should be in equal length.") |
|
53 |
+ } |
|
54 |
+ |
|
55 |
+ breaks <- c(breaks, to) |
|
56 |
+ labels <- c(labels, gsub("\\.", "", as.character(m$from))) |
|
57 |
+ |
|
58 |
+ if (!is.null(mrsd) && class(plot$data$x) == "Date") { |
|
59 |
+ obj <- scale_x_date(breaks=decimal2Date(breaks), labels) |
|
60 |
+ } else { |
|
61 |
+ obj <- scale_x_continuous(breaks=breaks, labels=labels) |
|
62 |
+ } |
|
63 |
+ ggplot_add(obj, plot, object_name) |
|
64 |
+} |
... | ... |
@@ -34,15 +34,23 @@ xlim_expand <- function(xlim, panel) { |
34 | 34 |
##' @method ggplot_add facet_xlim |
35 | 35 |
##' @export |
36 | 36 |
ggplot_add.facet_xlim <- function(object, plot, object_name) { |
37 |
- var <- quo_name(plot$facet$params$cols[[1]]) |
|
37 |
+ facet_col <- plot$facet$params$cols |
|
38 |
+ var <- quo_name(facet_col[[1]]) |
|
39 |
+ |
|
38 | 40 |
free_x <- plot$facet$params$free$x |
39 |
- if (!is.null(free_x) && !free_x) { |
|
40 |
- message('If you want to adjust xlim for specific panel, you need to set `scales = "free_x"`') |
|
41 |
+ if (!is.null(free_x)) { |
|
42 |
+ if (!free_x) |
|
43 |
+ message('If you want to adjust xlim for specific panel, you need to set `scales = "free_x"`') |
|
41 | 44 |
} |
45 |
+ |
|
42 | 46 |
class(object) %<>% extract(., .!= "facet_xlim") |
43 |
- nm <- names(object$data) |
|
44 |
- nm[nm == '.panel'] <- var |
|
45 |
- names(object$data) <- nm |
|
47 |
+ |
|
48 |
+ if (!is.null(facet_col)) { |
|
49 |
+ nm <- names(object$data) |
|
50 |
+ nm[nm == '.panel'] <- var |
|
51 |
+ names(object$data) <- nm |
|
52 |
+ } |
|
53 |
+ |
|
46 | 54 |
ggplot_add(object, plot, object_name) |
47 | 55 |
} |
48 | 56 |
|
... | ... |
@@ -1,23 +1,21 @@ |
1 | 1 |
% Generated by roxygen2: do not edit by hand |
2 |
-% Please edit documentation in R/experimental_function.R |
|
2 |
+% Please edit documentation in R/scales.R |
|
3 | 3 |
\name{scale_x_ggtree} |
4 | 4 |
\alias{scale_x_ggtree} |
5 | 5 |
\title{scale_x_ggtree} |
6 | 6 |
\usage{ |
7 |
-scale_x_ggtree(tree_view, breaks = NULL, labels = NULL) |
|
7 |
+scale_x_ggtree(breaks = waiver(), labels = waiver()) |
|
8 | 8 |
} |
9 | 9 |
\arguments{ |
10 |
-\item{tree_view}{tree view} |
|
11 |
- |
|
12 | 10 |
\item{breaks}{breaks for tree} |
13 | 11 |
|
14 | 12 |
\item{labels}{lables for corresponding breaks} |
15 | 13 |
} |
16 | 14 |
\value{ |
17 |
-tree view |
|
15 |
+updated tree view |
|
18 | 16 |
} |
19 | 17 |
\description{ |
20 |
-scale x for tree with heatmap |
|
18 |
+scale x for tree with gheatmap |
|
21 | 19 |
} |
22 | 20 |
\author{ |
23 | 21 |
Guangchuang Yu |