I used grid.table from the package gridExtra in R to make a PDF report of my Stat tests outputs.
I use this code:
library(gridExtra)
my_text = readLines("Dunnett.txt")
my_text2 = readLines("Shapiro-Wilk.txt")
pdf(sprintf("Results.pdf"), width=11, height=8)
grid.table(my_text)
grid.table(my_text2)
dev.off()
#cleanup
file.remove("Dunnett.txt")
file.remove("Shapiro-Wilk.txt")
But the problem is that my grid.table1 and 2 overlay on each other in one page. I want them be saved in 2 different pages.
Does anybody know how to do that?
library(grid)
grid::grid.newpage()
Related
I have at least 10 plots by ggplot(we can call them plot1, plot2 ....). I can output them into separate pdf files. But I prefer to output them in only one pdf file but several pages. One page, one plot from ggplot.
I tried to list all plots and use ggsave but it can not work. Any idea or script can help? Thank you
See the pdf function for this.
For three plots it would look like this (saving into your working directory with default naming). Run through dev.off line before you can open file.
pdf()
plot1
plot2
plot3
dev.off()
If your plots are already stored in a list named list1:
pdf()
list1
dev.off()
Based on aosmith's answer, here's a simple wrapper function to save lists of ggplot2 plots to a single pdf.
GG_save_pdf = function(list, filename) {
#start pdf
pdf(filename)
#loop
for (p in list) {
print(p)
}
#end pdf
dev.off()
invisible(NULL)
}
Having an unusual problem with creating multiple files in R with ggplot2.
I've got multiple plots to create for multiple people, so I'm creating all the plots for each person in a pdf. So it goes something like this...
for(i in 1:10)
{
pdf(paste("person",i,".pdf",sep=""))
ggplot2(...)+.........
ggplot2(...)+.........
ggplot2(...)+.........
ggplot2(...)+.........
dev.off()
}
I've verified that all the code to create the plots is working and that creating a single pdf works, no problems there. The problem arises when I try to run the loop, it creates the files, but they're blank. I've tried everything I can think of and can't seem to find any information about this. I've tried in RStudio (Windows) and command line (ubuntu), both create the same issue.
Any insight or an alternative would be appreciated, thanks
You need to use print for each plot want you output into a pdf.
library(ggplot2)
dat = data.frame(x1=rnorm(10), x2=rnorm(10))
for(i in 1:2){
pdf(paste("person",i,".pdf",sep=""))
p1 = ggplot(dat, aes(x=x1)) + geom_histogram()
p2 = ggplot(dat, aes(x=x2)) + geom_histogram()
print(p1)
print(p2)
dev.off()
}
I need to save plots from R as EMF format (windows metafile format) because this makes the chart look good on screen and paper in Microsoft Word. No other option (PNG, postscript etc) works well on both. The PNG device produces poor res plots. Tinkering with res parameters blows up the graph elements and I can't find anything that clearly explains how to mitigate this. Using postscript print output is pretty good. However, Word's EPS filters are busted so that I can't see the EPS file on screen. I need something that works well on screen and on paper. win.metafile is only thing that does both.
Here's the twist. I am using gridExtra to customise the layout of my plots. From what I gather, this means that I am writing multiple plots onto one device (which I then want to export to EMF). But I know that win.metafile only allows one plot per file. From ?win.metafile:
For win.metafile only one plot is allowed per file
So the following shouldn't work:
library(ggplot2)
library(gridExtra)
# g_legend pinched from Hadley:
# https://github.com/hadley/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs
g_legend <- function(a.gplot)
{
tmp <- ggplot_gtable(ggplot_build(a.gplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
return(legend)
}
win.metafile(file='test.emf', width=6, height=4)
p <- ggplot(mtcars, aes(x=cyl, y=mpg, colour=factor(gear)))
pl <- p + geom_point()
legend <- g_legend(pl)
lwidth <- sum(legend$width)
pp <- arrangeGrob(pl + theme(legend.position="none"), legend)
pp
dev.off()
In fact I get the following error message:
Error in grid.newpage() : metafile 'test.emf' could not be created
Ok. So here's my question: how can I trick win.metafile to see only one plot from the arrangeGrob output? Can I stuff its output into something and get one plot out? It must be possible because if I use RStudio's export function, I get an excellent looking chart on screen and paper. But I want to codify this so I don't have to manually export the files.
I've scoured the web and haven't been able to find anything that addresses this. Help would be greatly appreciated!
I tried this just now using the devEMF package, and though it throws a warning it looks like the picture that you've created here.
You just need to install.packages('devEMF') and then:
require(devEMF)
emf('imPic.emf')
print(pp)
dev.off()
I'm trying to render a plot to a PDF using the following approach:
pdf('~/Desktop/test.pdf', bg = "white", paper="USr")
p <- ggplot(df, aes(something)) + geom_bar();
print(p)
# I'm actually printing a bunch of graphs to the PDF
dev.off()
The "USr" in the PDF function is setting up the PDF to print in landscape mode. The plot is produced and is centered on the page but there is a large right/left margin and the plot isn't scaling out to take up the full 11" available to it.
I've tried some tweaks to the pdf(...) command and to the ggplot itself. Is there a solution this way or do I need to use a dedicated reporting/pdf package like sweave or knitr?
See this discussion; bottom-line is you probably want to use paper=special and set width and height explicitly.
Edit:
Here's a lazy trick to use ggsave with multiple pages,
library(ggplot2)
plots = replicate(8, qplot(1,1), simplify=FALSE)
library(gridExtra)
p <- do.call(marrangeGrob, c(plots,ncol=1,nrow=1))
ggsave("multipage.pdf", p, width=11, height=8.5)
(but otherwise, pdf(...) followed by a for loop is just fine and sometimes clearer)
I am using the function plotMDS() of package limma that makes a plot by the simple plot() format of R, and also returns the position of the points on the plot as output. I want to use the output of plotMDS() to produce my own beautiful plot.
Is there any way to run plotMDS() without having it's plot really generated? The reason I ask so is that I have already casted the output to a PDF file and I don't want the original plot of the plotMDS() to be there!
Thanks #BenBolker, it can be done like this:
pdf("Some file")
...
dev.new() # Putting new plots to nowhere
mds <- plotMDS(data)
dev.off() # Restoring new plots to the PDF file
plot(...) # Making the desired plot using mds
...
dev.off() # Closing PDF file
Looking at your answer it seems like this might be a reasonable alternative:
mds <- plotMDS(data)
pdf("Some file")
...
plot(...) # Making the desired plot using mds
...
dev.off() # Closing PDF file
I don't know exactly what you're doing but if you're interested in reproducible documents then you could also use the knitr package to create your output. It would be very easy to suppress a single plot and then plot later using knitr.