I'm simply trying to print the current figure in Octave to a .png file using the print() function. The documentation seems pretty straightforward, but it's not working. I get no error messages, but the files are nowhere to be found. I am doing
filename = sprintf('/home/me/Desktop/file_%d.png',n);
print(filename, '-dpng');
where n is just some loop counter variable. Again, I get no error, but when I check /home/me/Desktop/, there are no files. Am I doing this wrong?
Octave probably doesn't know where your current figure is or the filename is bad. Try using this version of print
print (h, filename, options)
with h given for the plot figure handle. Also try printing the filename to console and make sure it is correct
Related
I am calling one R Markdown script from another R script.Below you can see command
rmarkdown::render((file=paste(path1,"/Dashboard.Rmd",sep="")),params=list(args = myarg))
The script is executed without any problem but is not open automatically.
So can anybody help me how to solve this problem and open this script automatically after running of this command ?
First, your syntax probably isn't doing what you intended. Writing
rmarkdown::render((file=paste(path1,"/Dashboard.Rmd",sep="")),params=list(args = myarg))
will create a new variable named file and use it as the first parameter to rmarkdown::render. A more likely way to get what you want is to write it as
outfile <- rmarkdown::render(paste(path1,"/Dashboard.Rmd",sep=""),
params=list(args = myarg))
This removes the assignment from the first argument, and saves the
result (which is the name of the file that was produced).
Now, on to your question: You need to follow that line with
rstudioapi::viewer(outfile)
to view it in RStudio, or
browseURL(outfile)
elsewhere, because rmarkdown::render doesn't automatically call a previewer.
R newbie question: I am generating PDFs using rmarkdown from the console (not using rstudio). I have written a simple r script to render the rmarkdown file from the console, it basically looks like this:
# my_r_script.R
rmarkdown::render('mydoc.Rmd', output_file = opt$out,
params = list(
something = opt$something,
else = opt$else
)
)
In the rmd file bad errors might happen, e.g. some calculations might crash due to the given parameters. Question How can I access those errors in the R script? Or in other words: I want to know if something went wrong in the RMD file how could I achieve that?
You can wrap the rmarkdown::render statement in a try catch function - there is a great example here.
You should be able to store the output in a variable for further debugging.
I'm making a simple line in r to automatically open my generated plots.
I output the plots to a file called "plots.pdf" in the same directory as my r file, and at the end i use this two lines to try to open it:
dir <- paste("/Applications/Skim.app/Contents/MacOS/Skim ",getwd(),"/plots.pdf",sep="")
system(dir)
Basically, dir concatenates the full path of the skim app and the full path of the generated plot.
If i run the string stored at dir in a shell it works perfect, it opens the pdf file in Skim, but when i run it with system() from inside R it doesn't work (Skim says 'The document “plots.pdf” could not be opened.').
I believe this is a very little mistake somewhere in the syntax regarding the absolute/relative paths, but haven't managed to find it... Any advice is welcome! (Or a better way to achieve the same)
I found a way to bypass that problem, i just changed the path to Skim for the 'open' command and i let the system to assign the default app for pdf viewing. So:
dir <- paste("open ",getwd(),"/plots.pdf",sep="")
And it works.
Lets say I want to use sink for writing to a file in R.
sink("outfile.txt")
cat("Line one.\n")
cat("Line two.")
sink()
question 1. I have seen people writing sink() at the end, why do we need this? Can something go wrong when we do not have this?
question 2. What is the best way to write many lines one by one to file with a for-loop, where you also need to format each line? That is I might need to have different number in each line, like in python I would use outfile.write("Line with number %.3f",1.231) etc.
Question 1:
The sink function redirects all text going to the stdout stream to the file handler you give to sink. This means that anything that would normally print out into your interactive R session, will now instead be written to the file in sink, in this case "outfile.txt".
When you call sink again without any arguments you are telling it to resume using stdout instead of "outfile.txt". So no, nothing will go wrong if you don't call sink() at the end, but you need to use it if you want to start seeing output again in your R session/
As #Roman has pointed out though, it is better to explicitly tell cat to output to the file. That way you get only what you want, and expect to see in the file, while still getting the rest ouf the output in the R session.
Question 2:
This also answers question two. R (as far as I am aware) does not have direct file handling like in python. Instead you can just use cat(..., file="outfile.txt") inside a for loop.
I am using R or starting to use R. I did some script using for loops, if... and I am happy with the results.
Now the issue I have is that in the console I would have all the line of codes (around 150 lines) when really I am just interested in 4 lines, my results.
Is there anyway to clean the console to see only some requested lines? and not all of the codes? If not I am thinking about saving them in a csv file and access the csv file to see the results of the script but it is not really efficient.
Thanks in advance
Xavier
I expect this to depend on how your 'results' are in the console, and whether all the rest is truly 'code'. Are these 4 lines the result of cat/print statements? Then you could look at ?sink to send the results to a file.
Another option is to store these results in a variable (e.g. a list), and at the end of all your calculations, print this list. after that it should be easy to do the separation.
You are writing code in a script editor and not in the console right? Another option would be to use source() on the script which will run the entire script but won't show in the console (only the output). RStudio (which I strongly recommend you use for R; http://rstudio.org/) has a "source this file" button or something like that.
But more importantly, getting R to clearly return the results is a big part of learning how to program in R. You want your scripts to be clear for others as well! Some solutions would be to make some code chunks a function or as Nick suggested storing results in a list.
For me, I would put your code into a function, which would effectively hide the code from the console as it is run, and store the results of the code into a variable and then save that to a file
foo <- function(x) {
result<-0
for(i in 1:length(x)){
result<-result+x[i]
}
return(result)
}
bar <- foo(x=c(2,3,4,5,4,3,2,3,4,5))
write.csv(bar, "resultfile.csv")