CODEWITHSUNDEEP
rimageggplot2save
GodinA
GodinA

Reputation: 1093

Saving multiple ggplots from ls into one and separate files in R

I have several ggplots as objects on my ls. I want to save them as separate files (although I would also be interested to know how to save them all under 1 big file). I have read this: question and question but I can't seem to adapt the code. I also tried to plot them all in one big file as suggested here but do get this error: Error in do.call("grid.arrange", plots2[[i]]) : second argument must be a list. There's something that I am missing in getting all the ggplots in one list.

This is what I've tried so far:

> ls() #List of objects on my ls. All the p* are my ggplots that I want to save.
[1] "all"     "dat"     "dat2"    "dat3"    "data"    "dlook"   "dlook2"  "dlook3"  "i"       "look2"   "mdfx"   
[12] "objects" "order"   "p"       "p1"      "p10"     "p11"     "p12"     "p13"     "p14"     "p15"     "p16"    
[23] "p17"     "p18"     "p19"     "p2"      "p3"      "p4"      "p5"      "p6"      "p7"      "p8"      "p9"    

> objects<-ls()
> plot<-objects[14:30]
> plots
 [1] "p1"  "p10" "p11" "p12" "p13" "p14" "p15" "p16" "p17" "p18" "p19" "p2"  "p3"  "p4"  "p5"  "p6"  "p7"  "p8"  "p9" 

> class(plots)
[1] "character"

plots2<-as.list(plots)#Transform into a list. 

library(gridExtra) #Code suggested to create one pdf file.
pdf("test.pdf", onefile = TRUE)
for (i in seq(length(plots2))) {
  do.call("grid.arrange", plots2[[i]])  
}
dev.off()

Upvotes: 28

Views: 50928

Answers (4)

baptiste
baptiste

Reputation: 77096

It's best to have your plots in a list

l = mget(plots)

Then you can simply print them page-by-page,

pdf("all.pdf")
invisible(lapply(l, print))
dev.off()

or save one plot per file,

invisible(mapply(ggsave, file=paste0("plot-", names(l), ".pdf"), plot=l))

or arrange them all in one page,

   # On Windows, need to specify device
    ggsave("arrange.pdf", arrangeGrob(grobs = l), device = "pdf")

or arrange them 2x2 in multiple pages,

  # need to specify device on Windows 
    ggsave("arrange2x2.pdf", marrangeGrob(grobs = l, nrow=2, ncol=2),
device = "pdf")

etc.

(untested)

Upvotes: 62

Rtist
Rtist

Reputation: 4205

Note that you don't have to work with lapply. Suppose you have a list containing all your plots: 

MyPlots = list(plot1, plot2, plot3)

Just use:

pdf("all.pdf")
MyPlots
dev.off()

Upvotes: 13

Gregor Thomas
Gregor Thomas

Reputation: 145775

As an example fleshing out Joran's comment, and a supplement to Baptiste's answer, this is how you would initialize a list and store plots in a list up-front:

plots <- list()
plots[[1]] <- ggplot(...) # code for p1
plots[[2]] <- ggplot(...) # code for p2

## Depending on if your plots are scriptable, you could use a loop

for (i in 3:10) {
    plots[[i]] <- ggplot(...) # code for plot i
}

Then this list, plots, corresponds to l in baptiste's answer.

When using lists, single brackets, [, are used for sublists, where you have to use double brackets [[ to get the element of a list. For example, plots[[1]] will give you the ggplot object that is the first element of plots, but plots[1] will give you a length one list containing that first plot as an element. This may seem confusing at first, but it makes sense, especially if you just wanted to plot the first three plots, then you could use myplots[1:3] instead of l in any of baptiste's examples. (See ?"[" for more details.)

Whenever you catch yourself naming variables sequentially with numbers, e.g., x1, x2, x3, it's a good indication that you should be using a list instead.

Upvotes: 6

jlhoward
jlhoward

Reputation: 59355

If the plots p1, p10, etc. already exist, and you want them saved as p1.pdf, etc., then I think this should do it:

lapply(plots,function(x){ggsave(file=paste(x,"pdf",sep="."),get(x))})

ggsave(...) has a number of arguments for specifying the dimensions and format of the output file.

Upvotes: 6

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