since I read a lot similar question on stackoverflow so far, I couldn't find a good solution without updating ggplot2 to the development version.
My problem, I have several scripts which use arrangeGrob
to create combined graph out of individual graphs. I save them into a variable and print
this variable and/or save it with ggsave
. Since a lot of my colleagues update there packages regularly (which is a good thing I think), I always get mails my script no longer work after updating to gridExtra 2.0.0
.
I am not sure how to handle this, since the new ggplot2
version where the problem is solved is still under development. I found an article on stack overflow to remove a test if the object to save is a ggplot
since the new arrangeGrob
function returns a gtable
object, but this fails in my case:
library(ggplot2)
library(grid)
library(gridExtra)
a <- data.frame(x=c(1,2,3),
y=c(2,3,4))
p <- ggplot(a, aes(x, y)) + geom_point()
b <- arrangeGrob(p, p)
grid.draw(b)
ggsave('test.pdf', b)
ggsave <- ggplot2::ggsave
body(ggsave) <- body(ggplot2::ggsave)[-2]
ggsave('test.pdf', b)
Some output and error on the console:
d> grid.draw(b)
d> ggsave('test.pdf', b)
Error in ggsave("test.pdf", b) : plot should be a ggplot2 plot
d> ggsave <- ggplot2::ggsave
d> body(ggsave) <- body(ggplot2::ggsave)[-2]
d> ggsave('test.pdf', b)
Saving 10.5 x 10.7 in image
TableGrob (2 x 1) "arrange": 2 grobs
z cells name grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (2-2,1-1) arrange gtable[layout]
d>
The test.pdf
is created but it is corrupted in any way and can not be opened. Also the gtable
object get printed. So I guess something is wrong here.
But, as you can see, I found in the example code, I found the grid.draw
function to plot at least my combined graph but I still can not ggsave
it after the modification.
I don't want to use the "old" ( pdf(file = "test.pdf"); grid.draw(b); dev.off()
) device saving functions as suggested in this article , since they are very uncomfortable to use.
In this question someone asked exactly how to save the object, but in the answer they just explain to use grid.darw
and he accepted the answer as solving the problem
and nobody answered on my comments so far.
So I am pretty lost at the moment, how to provide working scripts for those who have and have not updated to new gridExtra
package. The way to remove the test within the ggsave
function is I guess the best solution since I can check the gridExtra
and ggplot2
version and just overwrite the ggsave
function in case there version do not match, but I could not get it to run.
Looking forward to get some help.
EDIT:
maybe the sessionInfo
helps
d> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridExtra_2.0.0 ggplot2_1.0.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 digest_0.6.8 MASS_7.3-44 plyr_1.8.3 gtable_0.1.2
[6] magrittr_1.5 scales_0.3.0 stringi_1.0-1 reshape2_1.4.1 devtools_1.9.1
[11] proto_0.3-10 tools_3.2.0 stringr_1.0.0 munsell_0.4.2 colorspace_1.2-6
[16] memoise_0.2.1
As an temporary workaround for this unfortunate transition period, you could re-implement the class hack that used to be in gridExtra,
class(b) <- c("arrange","ggplot", class(b))
print.arrange <- function(x) grid.draw(x)
ggsave('test.pdf', b)
Pascal brought me finally to the idea to check for the differences between ggplot 1.0.1
and ggplot 1.0.1.9003
, since I don't want to or force the development version of ggplot
.
So my idea is a function which will be executed within each script which overwrites the default ggsave
function.
I tested it now a little, if there are any bugs or so, please let me know. But the way I do it now it works so far.
repairGgsave <- function() {
ggplot_version <-
compareVersion(as.character(packageVersion('ggplot2')),
'1.0.1.9003')
gridextra_version <-
compareVersion(as.character(packageVersion('gridExtra')),
'0.9.1')
if(gridextra_version > 0) {
if(ggplot_version <= 0) {
ggsave <- function(filename, plot = last_plot(),
device = NULL, path = NULL, scale = 1,
width = NA, height = NA, units = c("in", "cm", "mm"),
dpi = 300, limitsize = TRUE, ...) {
dev <- plot_dev(device, filename, dpi = dpi)
dim <- plot_dim(c(width, height), scale = scale, units = units,
limitsize = limitsize)
if (!is.null(path)) {
filename <- file.path(path, filename)
}
dev(file = filename, width = dim[1], height = dim[2], ...)
on.exit(utils::capture.output(grDevices::dev.off()))
grid.draw(plot)
invisible()
}
assign("ggsave", ggsave, .GlobalEnv)
plot_dim <<- function(dim = c(NA, NA), scale = 1, units = c("in", "cm", "mm"),
limitsize = TRUE) {
units <- match.arg(units)
to_inches <- function(x) x / c(`in` = 1, cm = 2.54, mm = 2.54 * 10)[units]
from_inches <- function(x) x * c(`in` = 1, cm = 2.54, mm = 2.54 * 10)[units]
dim <- to_inches(dim) * scale
if (any(is.na(dim))) {
if (length(grDevices::dev.list()) == 0) {
default_dim <- c(7, 7)
} else {
default_dim <- dev.size() * scale
}
dim[is.na(dim)] <- default_dim[is.na(dim)]
dim_f <- prettyNum(from_inches(dim), digits = 3)
message("Saving ", dim_f[1], " x ", dim_f[2], " ", units, " image")
}
if (limitsize && any(dim >= 50)) {
stop("Dimensions exceed 50 inches (height and width are specified in '",
units, "' not pixels). If you're sure you a plot that big, use ",
"`limitsize = FALSE`.", call. = FALSE)
}
dim
}
plot_dev <<- function(device, filename, dpi = 300) {
if (is.function(device))
return(device)
eps <- function(...) {
grDevices::postscript(..., onefile = FALSE, horizontal = FALSE,
paper = "special")
}
devices <- list(
eps = eps,
ps = eps,
tex = function(...) grDevices::pictex(...),
pdf = function(..., version = "1.4") grDevices::pdf(..., version = version),
svg = function(...) grDevices::svg(...),
emf = function(...) grDevices::win.metafile(...),
wmf = function(...) grDevices::win.metafile(...),
png = function(...) grDevices::png(..., res = dpi, units = "in"),
jpg = function(...) grDevices::jpeg(..., res = dpi, units = "in"),
jpeg = function(...) grDevices::jpeg(..., res = dpi, units = "in"),
bmp = function(...) grDevices::bmp(..., res = dpi, units = "in"),
tiff = function(...) grDevices::tiff(..., res = dpi, units = "in")
)
if (is.null(device)) {
device <- tolower(tools::file_ext(filename))
}
if (!is.character(device) || length(device) != 1) {
stop("`device` must be NULL, a string or a function.", call. = FALSE)
}
dev <<- devices[[device]]
if (is.null(dev)) {
stop("Unknown graphics device '", device, "'", call. = FALSE)
}
dev
}
}
}
}
It basically overwrites the ggsave
and creates two new functions from the development version.
After executing the function everything seems to work.
修复我明确定义文件:
ggsave(file='test.pdf', b)
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