I am currently using the rgl package for some data representation.
Here's my command
mypath("directory")
png(file=mypath, res=600, width=10.5, height= 10.5,units="in",bg = "transparent")
require(rgl)
set.seed(1)
df <- data.frame(replicate(4,sample(1:200,1000,rep=TRUE)))
colnames(df) <- c("var1","var2","var3","var4")
plot3d(x=df$var1, y=df$var2, z=df$var3, col=as.numeric(df$var4), size=0.5, type='s',xlab="var1",ylab="var2",zlab="var3")
rgl.snapshot(mypath)
The command above works and produces a tiny image, which I wasn't able to make bigger, or increase its resolution (to 600).
I have also tried to export a pdf using:
rgl.postscript(mypath, fmt="pdf")
but when I execute the command R goes into a "not responding" state.
Can somebody please show me how to properly export the file? I would prefer the have the PNG with the resolution 600 dpi.
Cheers,
A solution can be to set the size of the window using open3d() :
require(rgl)
set.seed(1)
df <- data.frame(replicate(4,sample(1:200,1000,rep=TRUE)))
colnames(df) <- c("var1","var2","var3","var4")
open3d(windowRect=c(100,100,700,700))
plot3d(x=df$var1, y=df$var2, z=df$var3, col=as.numeric(df$var4), size=0.5, type='s',xlab="var1",ylab="var2",zlab="var3")
rgl.snapshot(<path to png file>)
May be someone need. I used the following combination for persp3Drgl:
persp3Drgl(...)
par3d( windowRect=c( 0,0,100,100 ) )
snapshot3d( file.path(plotDir, "3D.png"), top = TRUE )
Without top = TRUE it got failed.
Related
I have a ggplot object. Let's call it plot. I would like to convert it to png format, but I don't want to save it to a file on my local drive. I'm trying to work with that png object but I want to keep everything in the environment. Everything I've found, including ggsave, appears to force one to save the image as a file on the local drive first. I know image files can be stored as values, but I can't seem to get over the "save as" image and "import" image steps.
Here's some code for repoducibility:
library(tidyverse)
df <- as.data.frame(Titanic)
gg <- ggplot(data = df, aes(x = Survived, y = Freq))
plot <- gg + geom_bar(stat = "identity")
Now, I'd like to convert plot to a png to png without having to save it to a file. Something like:
png <- save.png(plot)
Thanks for the help!
It looks like the goal here would be to convert plot (the ggplot object) directly to a Magick image that you can operate on with functions in the magick package. Something like this:
mplot = image_graph(width=400, height=500)
plot
dev.off()
image_graph opens a graphics device that produces a Magick image and assigns it to mplot so that you'll have the object available in your environment. Then, when you type mplot in the console, you'll see the following:
format width height colorspace matte filesize density
1 PNG 400 500 sRGB TRUE 0 +72x+72
However, when I try to display the mplot image (type mplot in the console), I see the following:
even though the original plot looks like this:
I'm not sure what's going wrong, but hopefully someone with greater familiarity with magick will drop by and provide a solution.
I was faced with a similar issue and followed #eipi12 approach of using magick. The code bellow should work:
library(ggplot2)
library(magrittr)
ggsave_to_variable <- function(p, width = 10, height = 10, dpi = 300){
pixel_width = (width * dpi) / 2.54
pixel_height = (height * dpi) / 2.54
img <- magick::image_graph(pixel_width, pixel_height, res = dpi)
on.exit(utils::capture.output({
grDevices::dev.off()}))
plot(p)
return(img)
}
p <- data.frame(x = 1:100, y = 1:100) %>%
ggplot(aes(x = x, y = y)) +
geom_line()
my_img <- ggsave_to_variable(p)
my_img %>%
magick::image_write("my_img.png")
I'm attempting to step through a dataset and create a histogram and summary table for each factor and save the output as a .svg . The histogram is created using ggplot2 and the summary table using summary().
I have successfully used the code below to save the output to a single .pdf with each page containing the relevant histogram/table. However, when I attempt to save each histogram/table combo into a set of .svg images using ggsave only the ggplot histogram is showing up in the .svg. The table is just white space.
I've tried using dev.copy Cairo and svg but all end up with the same result: Histogram renders, but table does not. If I save the image as a .png the table shows up.
I'm using the iris data as a reproducible dataset. I'm not using R-Studio which I saw was causing some "empty plot" grief for others.
#packages used
library(ggplot2)
library(gridExtra)
library(gtable)
library(Cairo)
#Create iris histogram plot
iris.hp<-ggplot(data=iris, aes(x=Sepal.Length)) +
geom_histogram(binwidth =.25,origin=-0.125,
right = TRUE,col="white", fill="steelblue4",alpha=1) +
labs(title = "Iris Sepal Length")+
labs(x="Sepal Length", y="Count")
iris.list<-by(data = iris, INDICES = iris$Species, simplify = TRUE,FUN = function(x)
{iris.hp %+% x + ggtitle(unique(x$Species))})
#Generate list of data to create summary statistics table
sum.str<-aggregate(Sepal.Length~Species,iris,summary)
spec<-sum.str[,1]
spec.stats<-sum.str[,2]
sum.data<-data.frame(spec,spec.stats)
sum.table<-tableGrob(sum.data)
colnames(sum.data) <-c("species","sep.len.min","sep.len.1stQ","sep.len.med",
"sep.len.mean","sep. len.3rdQ","sep.len.max")
table.list<-by(data = sum.data, INDICES = sum.data$"species", simplify = TRUE,
FUN = function(x) {tableGrob(x)})
#Combined histogram and summary table across multiple plots
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list,table.list))),
nrow=2, ncol=1, top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
#bypass the class check per #baptiste
ggsave <- ggplot2::ggsave; body(ggsave) <- body(ggplot2::ggsave)[-2]
#
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35),
top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
ggsave(filename,multi.plots)
#dev.off()
}
Edit removed theme tt3 that #rawr referenced. It was accidentally left in example code. It was not causing the problem, just in case anyone was curious.
Edit: Removing previous answer regarding it working under 32bit install and not x64 install because that was not the problem. Still unsure what was causing the issue, but it is working now. Leaving the info about grid.export as it may be a useful alternative for someone else.
Below is the loop for saving the .svg's using grid.export(), although I was having some text formatting issues with this (different dataset).
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35), top =quote(paste(iris$labels$Species,'\nPage', g,
'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
grid.draw(multi.plots)
grid.export(filename)
grid.newpage()
}
EDIT: As for using arrangeGrob per #baptiste's comment. Below is the updated code. I was incorrectly using the single brackets [] for the returned by list, so I switched to the correct double brackets [[]] and used grid.draw to on the ggsave call.
for(i in 1:3){
prefix<-unique(iris$Species)
prefix<-prefix[i]
multi.plots<-grid.arrange(arrangeGrob(iris.list[[i]],table.list[[i]],
nrow=2,ncol=1,top = quote(paste(iris$labels$Species))))
filename<-paste(prefix,".svg",sep="")
ggsave(filename,grid.draw(multi.plots))
}
I've been trying to make some very tiny line graphs using base plotting functions, but am coming unstuck when trying to add a thin border.
This is via RGui on Windows 7, saving a png from the plot window.
Here's my code:
dev.new(width=1.3,height=0.3)
par(mar=c(0,0,0,0))
set.seed(13)
x <- 1:10
y <- runif(10)
plot(x,y,type="n",xaxs="i",yaxs="i",ylim=c(0,1))
polygon( c(1,x,max(x),0), c(0,y,0,0), col="lightblue", border=NA)
lines(x,y,lwd=1)
Everything is fine until I try to add a box with a line width of 1, giving:
box(lwd=1)
Now I can solve this by increasing the line width to 2, but this seems a bit of a hack.
box(lwd=2)
Using rect like rect(1,0,10,1) doesn't seem to give me an appropriate solution either, with the bottom and right borders not being visible.
Have you considered giving mar a small non-zero value:
dev.new(width=0.3,height=0.3)
par(mar=c(0.01,0.01,0.01,0.01))
set.seed(13)
x <- 1:10
y <- runif(10)
plot(x,y,type="n",xaxs="i",yaxs="i",ylim=c(0,1))
polygon( c(1,x,max(x),0), c(0,y,0,0), col="lightblue", border=NA)
lines(x,y,lwd=1)
box(lwd=1)
I admit I haven't quite figured out what the end-game might be, but when I do an interactive "stretch" of that very small screen-object, it does result in an all-around border.
I do recognize that I am on a Mac and saving this to a pdf file and converting it to a png file for SO-inclusion may not be precisely reproducible on a Linux or Windows device.
Another solution base in grid and gridBase package. The idea is to replace the box by grid.rect.
Use gridBase to get the base viewport
Introduce some offset (viewport y ) to show the bottom line
Reduce the width of the viewport to show the right line.
Here my code:
library(gridBase)
sp <- baseViewports()
vp <- sp$plot
vp$width <- unit(0.999,'npc')
vp$y <- unit(0.001,'npc')
pushViewport(vp)
grid.rect(gp=gpar(fill=NA))
upViewport(1)
EDIT thanks to #baptiste, you can simply get the same result using only grid.rect:
library(grid)
grid.rect(width = unit(0.999,'npc'),
y = unit(0.5001, "npc"),
gp=gpar(fill=NA))
To answer my own question thanks to #baptiste's tip-off, this is a device dependent issue due to RGui. If the image is saved directly out to file using png everything works as intended. E.g.:
dev.new(width=1.3,height=0.3)
# repeat from here onwards only for png call below
par(mar=c(0,0,0,0))
set.seed(13)
x <- 1:10
y <- runif(10)
plot(x,y,type="n",xaxs="i",yaxs="i",ylim=c(0,1),bty="n")
polygon( c(1,x,max(x),0), c(0,y,0,0), col="lightblue", border=NA)
lines(x,y,lwd=1)
box(lwd=1)
Saving out to png from the "R Graphics" window gives my original stuffed up image:
Going directly to file using png like:
png("textbox_direct.png",width=116,height=27)
# take code block from above
dev.off()
...gives the correct result:
I'm trying to create a hard-copy image of a neural network graph and it keeps failing. If I try to create a PNG, nothing is generated, and if I try to generate a PDF I get a small file output that refuses to open with "file may be damaged" errors. If I just let it display in a graphics window, the image comes up fine.
I'm using 2.15.1 on OS X (10.7.4), built by Macports. The code I'm working with at the moment:
library(ALL)
library(neuralnet)
data(ALL)
ALL.pdat <- pData(ALL)
bt <- factor(substring(ALL.pdat$BT,1,1))
all.sds <- apply(exprs(ALL),1,sd)
top.10.sds <- rank(all.sds)>length(all.sds)-10
exprs.top.10 <- as.data.frame(t(exprs(ALL)[top.10.sds,]))
nn.data <- cbind(exprs.top.10, as.numeric(bt))
## Gene names start with a number, and that causes problems when trying to set up the
## formula for neuralnet.
col.names <- paste("g", colnames(nn.data), sep = '')
col.names[11] <- "bt"
colnames(nn.data) <- col.names
my.nn <- neuralnet(bt ~ g36108_at + g36638_at + g37006_at + g38096_f_at + g38319_at + g38355_at + g38514_at + g38585_at + g39318_at + g41214_at, nn.data, hidden = 10, threshold = 0.01)
summary(my.nn)
pdf("./nn-all.pdf")
plot.nn(my.nn)
dev.off()
png("./nn-all.png")
plot.nn(my.nn)
dev.off()
I've even rebooted the machine to make sure that all the memory is cleared up, and that didn't help any.
Simple reproducible example:
pdf("test.pdf")
set.seed(42)
plot(runif(20),rnorm(20))
png("test.png")
set.seed(42)
plot(runif(20),rnorm(20))
dev.off()
If I try to open the PDF with Adobe Reader on my German Windows 7, I get a nice informative error message telling me that the file cannot be opened because the file is in use by another application. This can be fixed easily:
pdf("test.pdf")
set.seed(42)
plot(runif(20),rnorm(20))
dev.off() #make sure to close the graphics device
png("test.png")
set.seed(42)
plot(runif(20),rnorm(20))
dev.off()
Edit:
The problem is plot.nn. Until the package gets patched, you need to redefine plot.nn manually as shown in this answer.
I'm creating charts using ggplot2 inside ODFWeave code chunks. I am setting the ODFWeave dimensions to 5x5in, but the graphs are being created at 480x480 px which looks like a default. How can I make these larger and match them to the ODF size to get a good quality print?
ODFWeave Options:
imageDefs <- getImageDefs()
imageDefs$dispWidth <- 5
imageDefs$dispHeight<- 5
setImageDefs(imageDefs)
Code snippet in weave doc:
<<ClosureGraph, echo = FALSE, fig = TRUE>>=
#function returns a ggplot obj.
p<-closuresbyperiod()
print(p)
#
Thanks to the package manager for pointing out that we can use plotWidth and Height to do this, e.g:
imageDefs <- getImageDefs()
imageDefs$dispWidth <- 4
imageDefs$dispHeight<- 4
imageDefs$plotWidth <- 800
imageDefs$plotHeight<- 800
setImageDefs(imageDefs)
This is done before issues the odfWeave command