I use org.rosuda.jri lib to run an R script that implements the ordinary kirging algorithm via java. I use ubuntu 13.04 and the version 1.7-3 of REngine While all the results are perfectly produced BUT i can not create the plots and store them.
while the following lines are perfectly executed in R console
png('/home/panisis/Desktop/plots/tralala.png');
spplot(df);
dev.off();
These ones are ignored
re.eval("png('/home/panisis/Desktop/plots/tralala.png');");
re.eval("spplot(df);");
re.eval("dev.off();");
What i am missing???
Thanks for the dedicated time. :-)
i just found the answer myself. i put it here for next users. i had to assign the plot to a temporary variable (like temp <- spplot()) and then use print(temp) to save it as png file for example temp <- spplot() png(filename="pathToFile") print(temp) dev.off()
Related
I am using the effects package in R to derive (and plot) the effects of a complicated linear model.
When I use allEffects(linearModel) I can see the results on screen and save it to a pdf file as usual. Since the model has many terms, the output is not useful as it stands.
Therefore I use effects(someTerm, linearModel) to focus on the terms of interest and the results on screen are what I need. However, when saving it to a pdf file, the file contains no useful output (though it does take up 3.5Kb of space). There is no error message from R at the console.
To ease understanding, I created a simple data set and a script for generating the effects plots, in the same way that I tried with the "real" model.
factorData.csv
A,B,C,y
a1,b1,c1,3
a1,b2,c1,4
a2,b1,c1,5
a2,b2,c1,6
a1,b1,c1,2
a1,b1,c2,3.5
a1,b2,c2,4
a2,b1,c2,5.1
a2,b2,c2,6.2
plotEffect.r
require(effects)
dataFile <- '/tmp/factorData.csv'
effectABfile <- '/tmp/effect_AB.pdf'
effectABCfile <- '/tmp/effect_ABC.pdf'
allEffectFile <- '/tmp/lm_eff.pdf'
df <- read.csv(file=dataFile,header=TRUE,sep=',')
linearModel <- lm(y~A*B*C,data=df)
lm_eff <- allEffects(linearModel)
pdf(file=effectABfile)
plot(effect('A:B',linearModel))
dev.off()
pdf(file=allEffectFile)
plot(lm_eff)
dev.off()
pdf(file=effectABCfile)
plot(Effect(c('A','B','C'),linearModel))
dev.off()
As you can see, I tried allEffects, effect and Effect; allEffects is the only one that works for me. Please note that the script assumes that the data is placed in /tmp/factorData.csv - you might need to change the path of course. I also randomised the order in which the plots are generated, with no effect.
I had a look elsewhere on stackoverflow and saving plots to pdfs fails was the closest but the advice there (to issue dev.off() after each plot to 'close' the pdf file) is something I do already, as seen in plotEffect.r.
I tried this script on 2 machines, each running Lubuntu 14.04.1 64-bit with R version 3.0.2 and the latest effects package installed within R using install.packages. The results were the same.
I would be very grateful for advice on how to fix the problem of saving (instances of) this plot type to a pdf.
Fix/workaround
As suggested by #Roland in the comments below, if you wish to save grid plots (such as the output from the effects plots in this instance) into pdf files, it is better/more reliable to generate the plots separately/manually (rather than in a script). It does not appear to be (as much of) an issue for base graphics or even ggplot2 graphics, where I for one have never encountered this problem/needed this workaround in the past. Thanks to #Roland for suggesting this fix!
#Roland also added that Sys.sleep() might help in scripts. Although it did not do so in my case, I discovered that it was possible to paste several such plotting commands and R would run them as a batch, saving the plots to pdf correctly. Therefore, I believe it should be possible to recover much of the benefits of running the script by taking these steps:
Use R to create the text representation of the pdf(), plot() and dev.off() triad of commands
The main script outputs this plotting command text (specific to each instance of a plot) to a file
Open the plotting command text in a text editor
Copy the entire contents of the commands file and paste it into the R console
Optionally, you may wish to use the command line in Step 3 and 4 - How can I load a file's contents into the clipboard? has useful advice.
This two stage procedure is a reasonable workaround, but arguably there should be no need for it.
I have a simple R script doing:
jpeg(myplot.jpg)
x<-seq(1,20,0.1)
y<-sin(x)
plot(x,y)
dev.off()
After execution it makes a myplot.jpg file in /root/work/ but renders gibberish information and does not plot a legible graph.
Also how can I view the graph in R shell itself?
The first argument to jpeg should be a character string, so I wouldn't expect your code to work unless myplot.jpg contained a character string. This works fine for me:
jpeg("myplot.jpg")
x<-seq(1,20,0.1)
y<-sin(x)
plot(x,y)
dev.off()
Whether you can view the graph in the "shell" depends on the R console you're using. If you're running R from bash, sh, etc, the answer is "no, you can't view a plot directly"... actually it wouldn't surprise me if there was a package that allowed you to create text-plots, but I don't think that's what you want.
I am using Ubuntu inside Windows XP using VirtualBox, and I installed R properly. I am using a library called psych for this. The following is my code:
impact <- read.table("stats1.ex.02.txt", header=T)
class(impact)
describe(impact)
I am taking Statistics One course on coursera.org and the Prof gives this txt file to work with. When I run this in R, using source("test.R") (where test.R is the filename I gave),
nothing happens. What could be problem here ?
Try using source("test.R", echo=TRUE) or adding print to whatever you want printed after sourcing your script. Thus, your script might be:
impact<- read.table("stats1.ex.02.txt",header=T)
print(class(impact))
print(describe(impact))
Is it possible to call the plot functions from the c++ ?
Currently when I try to do that, the ubuntu terminal sort of freezes for sometime ( may be the duration for which the 3d plot would be created and then rotated for a full 360 degrees) and then unfreezes, without ever popping a new window.
Is this the expected behavior or is there something that I am doing wrong ? How can I get the plots ( R graphics ) to run from within c++ using rinside and rcpp ?
Thnx
-Egon
Yes, there is a working examples in the Rcpp package. Look at the file functionCallback/newApiExample.r in the examples/ directory.
You may need to experiment with sleep() to 'hold' the plot for a moment, or plot to a file and then have the file displayed. It all depends but you gave little detail.
The environment variable which deals with the interactive session is R_INTERACTIVE_DEVICE.
We need to create a file named .Renviron in our home directory, and then add the following code to that file:
R_INTERACTIVE_DEVICE = X11 for Linux based systems.
anisha#linux-y3pi:~> ls .Renviron
.Renviron
anisha#linux-y3pi:~> cat .Renviron
R_INTERACTIVE_DEVICE = X11a
References:
1. http://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html
2. http://stat.ethz.ch/R-manual/R-patched/library/base/html/options.html
Is there an easy way to turn of all GUI elements in R and run it solely from the command line on OSX?
I'm trying to replicate the behavior of a remote linux terminal on my OSX machine. Thus plot() should just save a file and things like CRAN mirror selection should be text, not a Tk interface. I'm having trouble finding where to set this behavior.
I had this exact question and wanted a way to do it without changing my existing code. I usually run with graphics support but sometimes I'll run a script on the server for a larger dataset and then I just want the plots to be output somewhere automatically.
In Dirk's answer Ian Fellows gives the simple solution. On the command line in R type:
options(device=pdf)
And then any plots will be written to the current directly to an Rplots.pdf file.
If you want the files to not be plotted at all then use
options(device=NULL)
For the plots you can just direct the output to a file using the pdf() command (or png(), jpeg()...).
I don't own an OS X box, but did you try to unset the X11 environment variable DISPLAY:
DISPLAY="" R --vanilla
When I do that on Linux and query R for capabilties(), x11 comes up as FALSE as desired.
I don't run OSX but you could attempt to run R from the Terminal application, rather than the Mac OSX launcher, and see whether that runs as you need.
As Matti writes, you can send output to files using the following commands; but I don't know if that's really the substance of your question.
png("pngfile.png")
plot(foo)
title(main="bar")
dev.off()
So instead of the quartz graphical object, your output goes to the file.
Similarly, you can output what would normally appear in the terminal to a file.
sink("foo.file")