+161
-16
lines changedFilter options
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-16
lines changed Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
1 1
Package: ggtree
2 2
Type: Package
3 3
Title: a phylogenetic tree viewer for different types of tree annotations
4 -
Version: 1.1.16
4 +
Version: 1.1.17
5 5
Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
6 6
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
7 7
Description: ggtree extends the ggplot2 plotting system which implemented the
@@ -71,6 +71,8 @@ export(rtree)
71 71
export(scaleClade)
72 72
export(scale_color)
73 73
export(scale_x_ggtree)
74 +
export(subview)
75 +
export(theme_transparent)
74 76
export(theme_tree)
75 77
export(theme_tree2)
76 78
export(write.jplace)
@@ -129,6 +131,7 @@ importFrom(ggplot2,geom_segment)
129 131
importFrom(ggplot2,geom_text)
130 132
importFrom(ggplot2,geom_tile)
131 133
importFrom(ggplot2,ggplot)
134 +
importFrom(ggplot2,ggplotGrob)
132 135
importFrom(ggplot2,guide_legend)
133 136
importFrom(ggplot2,guides)
134 137
importFrom(ggplot2,labs)
@@ -1,3 +1,10 @@
1 +
CHANGES IN VERSION 1.1.17
2 +
------------------------
3 +
o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
4 +
o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
5 +
o theme_transparent to make background transparent <2015-08-27, Thu>
6 +
o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
7 + 1 8
CHANGES IN VERSION 1.1.16
2 9
------------------------
3 10
o update citation <2015-08-17, Mon>
@@ -36,7 +36,12 @@ ggplotGrob <- ggplot2::ggplotGrob
36 36
##' @param stat The statistical transformation to use on the data for this layer
37 37
##' @param position The position adjustment to use for overlapping points on this layer
38 38
##' @param parse if TRUE, the labels will be passd into expressions
39 +
##' @param show.legend logical
40 +
##' @param inherit.aes logical
39 41
##' @param ... other arguments passed on to 'layer'
42 +
##' @param nudge_x horizontal adjustment
43 +
##' @param nudge_y vertical adjustment
44 +
##' @param check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted
40 45
##' @source
41 46
##' This is just the imported function
42 47
##' from the ggplot2 package. The documentation you should
@@ -267,7 +267,7 @@ geom_tippoint <- function(...) {
267 267
theme_tree <- function(bgcolor="white", fgcolor="black", ...) {
268 268
theme_tree2() %+replace%
269 269
theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),
270 -
axis.line.x = element_line(color=bgcolor),
270 +
axis.line.x = element_blank(),
271 271
axis.text.x = element_blank(),
272 272
axis.ticks.x = element_blank(),
273 273
...)
@@ -301,12 +301,32 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {
301 301
panel.background=element_rect(fill=bgcolor, colour=bgcolor),
302 302
panel.border=element_blank(),
303 303
axis.line=element_line(color=fgcolor),
304 -
axis.line.y=element_line(color=bgcolor),
304 +
axis.line.y=element_blank(),
305 305
axis.ticks.y=element_blank(),
306 306
axis.text.y=element_blank(),
307 307
...)
308 308
}
309 309 310 +
##' transparent background theme
311 +
##'
312 +
##'
313 +
##' @title theme_transparent
314 +
##' @param ... additional parameter to tweak the theme
315 +
##' @return ggplot object
316 +
##' @importFrom ggplot2 theme
317 +
##' @importFrom ggplot2 element_rect
318 +
##' @export
319 +
##' @author Guangchuang Yu
320 +
theme_transparent <- function(...) {
321 +
theme(panel.background = element_rect(
322 +
fill = "transparent",
323 +
colour = NA),
324 +
plot.background = element_rect(
325 +
fill = "transparent",
326 +
colour = NA), ...)
327 +
}
328 + 329 + 310 330
##' hilight clade with rectangle
311 331
##'
312 332
##'
@@ -642,6 +662,7 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {
642 662
##'
643 663
##' @title add_legend
644 664
##' @param p tree view
665 +
##' @param width width of legend
645 666
##' @param x x position
646 667
##' @param y y position
647 668
##' @param offset offset of text and line
@@ -654,7 +675,7 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {
654 675
##' @importFrom ggplot2 ylim
655 676
##' @export
656 677
##' @author Guangchuang Yu
657 -
add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {
678 +
add_legend <- function(p, width=NULL, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {
658 679
dx <- p$data$x %>% range %>% diff
659 680 660 681
if (is.null(x)) {
@@ -666,14 +687,18 @@ add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {
666 687
p <- p + ylim(0, max(p$data$y))
667 688
}
668 689 669 - 670 -
d <- dx/10
671 -
n <- 0
672 -
while (d < 1) {
673 -
d <- d*10
674 -
n <- n + 1
690 +
if (is.null(width) || is.na(width)) {
691 +
d <- dx/10
692 +
n <- 0
693 +
while (d < 1) {
694 +
d <- d*10
695 +
n <- n + 1
696 +
}
697 +
d <- floor(d)/(10^n)
698 +
} else {
699 +
d <- width
675 700
}
676 -
d <- floor(d)/(10^n)
701 + 677 702
if (is.null(offset)) {
678 703
offset <- 0.4
679 704
}
@@ -10,6 +10,7 @@
10 10
##' @param high color of highest value
11 11
##' @param color color of heatmap cell border
12 12
##' @param colnames logical, add matrix colnames or not
13 +
##' @param colnames_position one of 'bottom' or 'top'
13 14
##' @param font.size font size of matrix colnames
14 15
##' @return tree view
15 16
##' @importFrom reshape2 melt
@@ -22,7 +23,10 @@
22 23
##' @export
23 24
##' @author Guangchuang Yu
24 25
gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",
25 -
color="white", colnames=TRUE, font.size=4) {
26 +
color="white", colnames=TRUE, colnames_position="bottom", font.size=4) {
27 + 28 +
colnames_position %<>% match.arg(c("bottom", "top"))
29 + 26 30
## if (is.null(width)) {
27 31
## width <- (p$data$x %>% range %>% diff)/30
28 32
## }
@@ -61,7 +65,12 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",
61 65
}
62 66 63 67
if (colnames) {
64 -
p2 <- p2 + geom_text(data=mapping, aes(x=to, label=from), y=0, size=font.size)
68 +
if (colnames_position == "bottom") {
69 +
y <- 0
70 +
} else {
71 +
y <- max(p$data$y) + 1
72 +
}
73 +
p2 <- p2 + geom_text(data=mapping, aes(x=to, label=from), y=y, size=font.size)
65 74
}
66 75 67 76
p2 <- p2 + theme(legend.position="right", legend.title=element_blank())
@@ -0,0 +1,26 @@
1 +
##' add subview to mainview for ggplot2 objects
2 +
##'
3 +
##'
4 +
##' @title subview
5 +
##' @param mainview main view
6 +
##' @param subview sub view
7 +
##' @param x x position
8 +
##' @param y y position
9 +
##' @param width width of subview, [0,1]
10 +
##' @param height height of subview, [0,1]
11 +
##' @return ggplot object
12 +
##' @importFrom ggplot2 annotation_custom
13 +
##' @importFrom ggplot2 ggplotGrob
14 +
##' @export
15 +
##' @author Guangchuang Yu
16 +
subview <- function(mainview, subview, x, y, width=.1, height=.1) {
17 +
xrng <- mainview$data$x %>% range %>% diff
18 +
yrng <- mainview$data$y %>% range %>% diff
19 + 20 +
mainview + annotation_custom(
21 +
ggplotGrob(subview),
22 +
xmin = x - width*xrng,
23 +
xmax = x + width*xrng,
24 +
ymin = y - height*yrng,
25 +
ymax = y + height*yrng)
26 +
}
Original file line number Diff line number Diff line change
@@ -4,11 +4,14 @@
4 4
\alias{add_legend}
5 5
\title{add_legend}
6 6
\usage{
7 -
add_legend(p, x = NULL, y = NULL, offset = NULL, font.size = 4, ...)
7 +
add_legend(p, width = NULL, x = NULL, y = NULL, offset = NULL,
8 +
font.size = 4, ...)
8 9
}
9 10
\arguments{
10 11
\item{p}{tree view}
11 12 13 +
\item{width}{width of legend}
14 + 12 15
\item{x}{x position}
13 16 14 17
\item{y}{y position}
@@ -10,7 +10,9 @@ read for the geom_text function can be found here: \link[ggplot2]{geom_text}
10 10
}
11 11
\usage{
12 12
geom_text(mapping = NULL, data = NULL, stat = "identity",
13 -
position = "identity", parse = FALSE, ...)
13 +
position = "identity", parse = FALSE, show.legend = NA,
14 +
inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0,
15 +
check_overlap = FALSE)
14 16
}
15 17
\arguments{
16 18
\item{mapping}{the aesthetic mapping}
@@ -24,7 +26,17 @@ only needed if you want to override he plot defaults.}
24 26 25 27
\item{parse}{if TRUE, the labels will be passd into expressions}
26 28 29 +
\item{show.legend}{logical}
30 + 31 +
\item{inherit.aes}{logical}
32 + 27 33
\item{...}{other arguments passed on to 'layer'}
34 + 35 +
\item{nudge_x}{horizontal adjustment}
36 + 37 +
\item{nudge_y}{vertical adjustment}
38 + 39 +
\item{check_overlap}{if TRUE, text that overlaps previous text in the same layer will not be plotted}
28 40
}
29 41
\description{
30 42
text annotations
@@ -5,7 +5,8 @@
5 5
\title{gheatmap}
6 6
\usage{
7 7
gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 -
color = "white", colnames = TRUE, font.size = 4)
8 +
color = "white", colnames = TRUE, colnames_position = "bottom",
9 +
font.size = 4)
9 10
}
10 11
\arguments{
11 12
\item{p}{tree view}
@@ -24,6 +25,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
24 25 25 26
\item{colnames}{logical, add matrix colnames or not}
26 27 28 +
\item{colnames_position}{one of 'bottom' or 'top'}
29 + 27 30
\item{font.size}{font size of matrix colnames}
28 31
}
29 32
\value{
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