I am running the package 'pophelper' in RStudio on a MacBookAir where I need to choose multiple files using file.choose(). However, when the interactive window pops up I can only highlight one file and not choose multiple files with the 'Shift' key. I've tried the 'control', 'option', 'command' key and any combination thereof but only managed to highlight one file at a time. I have to choose dozens of files so doing it one by one is not an option. Has anybody else encountered this issue and is there a solution to it?
Thanks for your help
From this question file.choose for multiple files R, you can use tk_choose.files() in tcltk package to choose a list of files interactively.
In addition, you can also make a custom function with select.list() and set multiple = T and graphics = T to call a graphical widget and select more than one item.
file.choose2 <- function(path = "."){
file <- dir(path)
select <- select.list(file, multiple = T, graphics = T)
return(file.path(path, select))
}
file.choose2("path/to/your/files")
The drawback of this function is that you can only select those files in the given path.
Related
I want to navigate to specific directories and process the files found within the folders. I have many models ('models') and experiment ('exps') combinations that I want to navigate to their specific directory and carry out processing on the data held within.
I can do this using:
models<- c("model1","model2","model3")
exps<- c("exp21","exp42","exp54")
for (g in 1:length(models)){
gfilepath = file.path("C:/Users/Documents/data/models",models[g],"Netcdfs")
for (r in 1:length(exps)){
rfilepath = file.path(gfilepath,exps[r])
list.files(rfilepath)
#Do my processing here
}
}
Can I do this without using a loop? I was looking at trying to use apply using just one vector of strings to incorporate in the file path:
test<-apply(c("model1","model2","model3"),function(x){
filename=file.path("C:/Users/Documents/data/models",x)
})
but I got:
Error in match.fun(FUN) : argument "FUN" is missing, with no default
I thought the 'file.path' would be the function?
Is it possible to navigate to the specific folders another way (besides for the loop)? I think maybe using a recursive option in a function may help, but I'm not sure.
The help file to list.files which can be accessed using ?list.files contains the argument you require, namely recursive = T
list.files(all.files = T, recursive = T)
I have been using officer package to create the respective PowerPoint decks, however at this moment, i would like to merge/ bind them all as one slide deck and was not able to figure out. Can someone guide me if there any package that helps to merge multiple PowerPoint decks into one.
I believe currently there are no functions or packages that do this in R, so I'll suggest you a few possible solutions that come to mind.
1: I believe you could use read_pptx() to read, say, a deck1 and a deck2 files. Then, loop through the slide indexes of deck2, and use those values to add_slide() into deck1. I think there's a function in officer called pptx_summary(), which converts a pptx R object into a tibble, but I'm not sure you could convert a tibble back to a pptx R object.
2: You could convert pptx files into pdf files, and use pdftools to join them.
When creating PowerPoint slides automatically via R (for example by using the PowerPoint export of R markdown), merging them with pre-manufactured fixed slides (for example explanations with elaborate visuals) may likely become necessary. As there seems not single-line solution so far, here's an incomplete answer to a 3-year-old question.
A look into the sources of OfficeR shows that the package works with a data structure and a temporary folder in the background that contains the XML files that are zipped in the XLSX file.
Copying slides, therefore, requires both: To update the structure, and to copy XML files and other ressources, eventually. Here is a very rough draft of how merging two PowerPoint files can work, based on the OfficeR classes.
merge_pptx = function(a, b, filename) {
# go through the slides of b
for (index in 1:length(source$slide$get_metadata())) {
# We need a new filename in the target's slide directory
new_slidename <- target$slide$get_new_slidename()
xml_file <- file.path(target$package_dir, "ppt/slides", new_slidename)
# Copy XML from source to new filename
orgFilename = source$slide$get_metadata()[index, "filename"]
newFilepath = paste(target$package_dir, newFilename, sep="/")
file.copy(orgFilename, xml_file)
# Not sure yet, what exactly this does
slide_info <- target$slideLayouts$get_metadata()[1,] # Use first best layout at the moment
layout_obj <- target$slideLayouts$collection_get(slide_info$filename)
layout_obj$write_template(xml_file)
# update presentation elements
target$presentation$add_slide(target = file.path("slides", new_slidename))
target$content_type$add_slide(partname = file.path("/ppt/slides", new_slidename))
# Add the slide to the collection
target$slide$add_slide(xml_file, target$slideLayouts$get_xfrm_data())
target$cursor <- target$slide$length()
}
print(target, target=filename)
}
source = read_pptx("One.pptx")
target = read_pptx("Two.pptx")
merge_pptx(source, target, "Combined.pptx")
Please note, that this is a draft only. It does not yet respect the different layouts for slides, not even speaking of different masters. Embedded files (images) are not yet copied.
The bulk of this function is inspired by the add_slide() function in the dir_slide class, see https://github.com/davidgohel/officer/blob/master/R/ppt_class_dir_collection.R
I've made different plots (more than a hundred) for a project and I haven't capture them on the way (yes it's bad , i know). Now, I need to save them all at once but without running again my script (which takes hours). Is there a way to do so within Rstudio ?
Edit: All the plot are already there and I don't want to run them again.
In RStudio, every session has a temporary directory that can be obtained using tempdir(). Inside that temporary directory, there is another directory that always starts with "rs-graphics" and contains all the plots saved as ".png" files. Therefore, to get the list of ".png" files you can do the following:
plots.dir.path <- list.files(tempdir(), pattern="rs-graphics", full.names = TRUE);
plots.png.paths <- list.files(plots.dir.path, pattern=".png", full.names = TRUE)
Now, you can copy these files to your desired directory, as follows:
file.copy(from=plots.png.paths, to="path_to_your_dir")
Additional feature:
As you will notice, the .png file names are automatically generated (e.g., 0078cb77-02f2-4a16-bf02-0c5c6d8cc8d8.png). So if you want to number the .png files according to their plotting order in RStudio, you may do so as follows:
plots.png.detials <- file.info(plots.png.paths)
plots.png.detials <- plots.png.detials[order(plots.png.detials$mtime),]
sorted.png.names <- gsub(plots.dir.path, "path_to_your_dir", row.names(plots.png.detials), fixed=TRUE)
numbered.png.names <- paste0("path_to_your_dir/", 1:length(sorted.png.names), ".png")
# Rename all the .png files as: 1.png, 2.png, 3.png, and so on.
file.rename(from=sorted.png.names, to=numbered.png.names)
Hope it helps.
Although this discussion has been inactive for a while, there are some persons, like myself, who still come across the same problem, and the other solutions don't really seem to even get what the actual question is.
So, hands on. Your plot history gets saved in a variable called .SavedPlots. You can either access it directly, assign it to another variable in code or do the latter from the plots window.
# ph for plot history
ph <- .SavedPlots
In R 3.4.2, I could index ph to reproduce the corresponding plot in a device. What follows is rather straightforward:
Open a new device (png, jpeg, pdf...).
Reproduce your plot ph[index_of_plot_in_history].
Close the device (or keep plotting if it is a pdf with multiple pages).
Example:
for(i in 1:lastplot) {
png('plotname.png')
print(ph[i])
dev.off()
}
Note: Sometimes this doesn't happen because of poor programming. For instance, I was using the MICE package to impute many datasets with a large number of variables, and plotting as shown in section 4.3 of this paper. Problem was, that only three variables per plot were displayed, and if I used a png device in my code, only the last plot of each dataset would be saved. However, if the plots were printed to a window, all the plots of each dataset would be recorded.
If your plots are 3d, you can take a snapshot of all your plots and save them as a .png file format.
snapshot3d(filename = '../Plots/SnapshotPlots.png', fmt = 'png')
Or else, the best way is to create a multi-paneled plotting window using the par(mfrow) function. Try the following
plotsPath = "../Plots/allPlots.pdf"
pdf(file=plotsPath)
for (x in seq(1,100))
{
par(mfrow = c(2,1))
p1=rnorm(x)
p2=rnorm(x)
plot(p1,p2)
}
dev.off()
You can also use png, bmp, tiff, and jpeg functions instead of pdf. You can read their advantages and disadvantages and choose the one you think is good for your needs.
I am not sure how Rstudio opens the device where the plot are drawn, but I guess it uses dev.new(). In that case one quick way to save all opened graphs is to loop through all the devices and write them using dev.print.
Something like :
lapply(dev.list(),function(d){dev.set(d);dev.print(pdf,file=file.path(folder,paste0("graph_",d,".pdf"))})
where folder is the path of the folder where you want to store your graph (could be for example folder="~" if you are in linux and want to store all your graph in your home folder).
If you enter the following function all that will follow will be save in a document:
pdf("nameofthedocument.pdf")
plot(x~y)
plot(...
dev.off()
You can also use tiff(), jpg()... see ?pdf
I'm using a kml package of R to cluster my data and I need to get in the end a csv file with a column including the number of clusters according to each id. The data has many missing values, so I can't use kmeans function without deleting all observations, but kml works nicely with that. My problem is that I use choice() to export the results and all I get is a graphical window, but no output files. Here is my code:
setwd("/Volumes/NATASHKA/api/R files")
statadata <-read.dta("Data_wide_withdemogr_auris_for_kml_negative.dta")
mydata <- data.frame(statadata)
cldDQ <- cld(mydata)
kml(cldDQ,c(2:6),20,toPlot="none")
plotAllCriterion(cldDQ)
par(mar = rep(2, 4))
X11(type = "Xlib")
choice(cldDQ, typeGraph = "bmp")
What do I do wrong?
I had the same problem and I solved it that way:
first, you need to choose the desired partition with the arrow
second, select it pressing “space”,
then press “Enter” and you can find all files in your work directory, check getwd().
Good luck.
I do a lot of data exploration in R and I would like to keep every plot I generate (from the interactive R console). I am thinking of a directory where everything I plot is automatically saved as a time-stamped PDF. I also do not want this to interfere with the normal display of plots.
Is there something that I can add to my ~/.Rprofile that will do this?
The general idea is to write a script generating the plot in order to regenerate it. The ESS documentation (in a README) says it well under 'Philosophies for using ESS':
The source code is real. The objects are realizations of the
source code. Source for EVERY user modified object is placed in a
particular directory or directories, for later editing and
retrieval.
With any editor allows stepwise (or regionwise) execution of commands you can keep track of your work this way.
The best approach is to use a script file (or sweave or knitr file) so that you can just recreate all the graphs when you need them (into a pdf file or other).
But here is the start of an approach that does the basics of what you asked:
savegraphs <- local({i <- 1;
function(){
if(dev.cur()>1){
filename <- sprintf('graphs/SavedPlot%03d.pdf', i)
dev.copy2pdf( file=filename )
i <<- i + 1
}
}
})
setHook('before.plot.new', savegraphs )
setHook('before.grid.newpage', savegraphs )
Now just before you create a new graph the current one will be saved into the graphs folder of the current working folder (make sure that it exists). This means that if you add to a plot (lines, points, abline, etc.) then the annotations will be included. However you will need to run plot.new in order for the last plot to be saved (and if you close the current graphics device without running another plot.new then that last plot will not be saved).
This version will overwrite plots saved from a previous R session in the same working directory. It will also fail if you use something other than base or grid graphics (and maybe even with some complicated plots then). I would not be surprised if there are some extra plots on occasion that show up (when internally a plot is created to get some parameters, then immediatly replaced with the one of interest). There are probably other things that I have overlooked as well, but this might get you started.
you could write your own wrapper functions for your commonly used plot functions. This wrapper function would call both the on-screen display and a timestamped pdf version. You could source() this function in your ~/.Rprofile so that it's available every time you run R.
For latice's xyplot, using the windows device for the on-screen display:
library(lattice)
my.xyplot <- function(...){
dir.create(file.path("~","RPlots"))
my.chart <- xyplot(...)
trellis.device(device="windows",height = 8, width = 8)
print(my.chart)
trellis.device(device = "pdf",
file = file.path("~", "RPlots",
paste("xyplot",format(Sys.time(),"_%Y%m%d_%H-%M-%S"),
".pdf", sep = "")),
paper = "letter", width = 8, height = 8)
print(my.chart)
dev.off()
}
my.data <- data.frame(x=-100:100)
my.data$y <- my.data$x^2
my.xyplot(y~x,data=my.data)
As others have said, you should probably get in the habit of working from an R script, rather than working exclusively from the interactive terminal. If you save your scripts, everything is reproducible and modifiable in the future. Nonetheless, a "log of plots" is an interesting idea.