I need to generate about >50 plots. I want to save them all in one pdf and have just a few of them appear in my R markdown html output.
I can print many plots to a single pdf like this:
pdf("path/to/out.pdf")
for (sam in samples){
plot(sam) # simplified stand-in for many lines of code
}
dev.off()
That puts one sample's plot on each page of a pdf that I can flip through later.
I want some of those plots to appear in my markdown, without duplicating the plot code.
I've tried:
pdf("path/to/out.pdf")
count=0
for (sam in samples){
plot(sam) # simplified stand-in for many lines of code
if (sample(1:10,1)==1){ #randomly select a few examples
count = count + 1
dev.copy(which=dev.prev()) # to revert back to the default device
dev.set(dev.next()) # to resume printing to the same pdf
}
}
dev.off()
With this, the pdf is correct and count is >0, but the plots do not appear in the markdown report.
I think something from the dev.copy() family will do what I want but I can't seem to make it work. In other variants I tried, dev.print() complains about only printing from a screen device, or I get errors saying that I cannot copy to the same device, or cannot copy to a null device.
Similar questions (such as Saving plot as pdf and simultaneously display it in the window (x11)) often want to do the reverse: print to screen a then to a pdf. And they generally only deal with one plot.
I want to make several plots, and I want ALL of my plots to go to the pdf, but only a FEW to go to the Rmarkdown html report as an example of what is in the pdf.
I'm working on a mac using R 3.5.1, RStudio v1.1.456
Thanks in advance!
Related
Is there any way to save the plots by code in RStudio?
Like something in Python save.plt().
I have noticed the function savePlot can save the figures but I cannot load it in RStudio, since it reports the errors in loading X11().
This leads me to think about another question... What is your way to using R or what is the proper way to using R? As a beginner I found RStudio is super easy to use and I like the idea that saving all the environments into a single file. But apparently it is no need to using X11() in plotting...
If you want to save from code the plot that is displayed in the RStudio plot tab then you have to call for example
rstudioapi::savePlotAsImage("test.png",width=300,height=150)
Plots can be saved as a jpg:
jpeg("Name_of_your_plot.jpg")
# your plot for example
plot(x,y)
dev.off()
Instead of jpg you can choose other image formats such as png, pdf or PostScript. The above code can be modified as:
png("Name_of_your_plot.png")
# your plot for example
plot(x,y)
dev.off()
If you have a ggplot you can use ggsave.
I was wondering if it is possible to set page labels in PDFs exported from R and import the PDF page as an image using said labels into LaTeX?
What I want to do is:
export several graphs from R to a single multi-page PDF file
label the pages in the PDF
Idea:
PDF("multipage.pdf")
graph_object_1 (label="bubblechart")
graph_object_2 (label="bargraph")
graph_object_3 (label="scatterplot")
dev.off()
import as graph into LaTeX using the label instead of a page number
\includegraphics[page={bargraph}]{multipage}
I am aware that I can access pages using the respective page number. But it is common that the graphs change over time, more are added, some are removed. And adapting the page numbers in the TeX file every time would be painful.
I know about Sweave and knitR but my co-authors don't use R and they are therefore not an option.
I am wondering why you want to use a single pdf file. Why not
pdf("bubblechart.pdf")
...
dev.off()
pdf("bargraph.pdf")
...
dev.off()
and then
\begin{figure}
\includegraphics{bubblechart}
\end{figure}
and so forth...
LaTeX would do all the numbering and you have maximal flexibility...
I am currently doing some statistical analysis in R and use knitr to generate results and an overview document.
There are some additional plots, which I want to be done and saved as a .png (with specified file name and location), but not included in the generated .html file (too many of them, and they are not at the end).
Using dev.copy(png, ...) works fine for generating the plots, but the figures appear in the .html. If I specify fig.keep=none the .png files are created, but blank.
Is there some way to do what I want?
This is from knitr website:
fig.show: ('asis'; character) how to show/arrange the plots; four
possible values are
asis: show plots exactly in places where they were
generated (as if the code were run in an R terminal)
hold: hold all
plots and output them in the very end of a code chunk
animate: wrap
all plots into an animation if there are mutiple plots in a chunk
hide: generate plot files but hide them in the output document
fig.show = 'hide' worked for me.
I have the following problem using R and not found a solution so far:
I have a script where I run several operation and generate some plots. At the end, I would like to have a nice piece of code that automatically saves all the plots generated into the current working directory. So far, I am using:
trellis.device(device="png", filename="Plot_A.png")
print(Plot_A)
dev.off()
Which is working fine for just one specific plot. Now I am looking for some kind of for loop that takes all the plots and saves them with the name of the plot as a png file
In grid based plotting packages (lattice and ggplot), you can store the plot in an object and call print on them to trigger actual rendering of the plot. What you could do is not render the image on the spot, but append any plots to a list. Then, at the end, you can loop over the plots and output them.
plot_list = list()
lattice_plot = xyplot()
plot_list = append(plot_list, lattice_plot)
for(plot in plot_list) {
png('name.png')
print(plot)
dev.off()
}
Not exactly an answer but an alternative workflow.
If you are saving your plots in order to use it somewhere else, for example to include them in a Word document or in a presentation, you could just put your code in an RMarkdown document and knitr it to generate an html or doc document with all the output generated by the code, including plots. With RStudio all that could be done with a few clicks.
It may even be easier to take all plots from the Word document than from a folder of png files.
I am producing a pdf plot with this kind of command:
ggplot(df, aes(sample = x))+
stat_qq(geom="point",distribution=qexp)+
geom_abline(intercept = 0, slope = 1,linetype='dashed',col='red')
ggsave(file="xxx.pdf")
Than I want to integrate the pdf into a tex file and produce a final pdf document.
But, the ggplot is very slow to display and makes the pdf crash very often.
When I use geom='line' it doesn't happen so I guess it comes from the number of circle points.
Do you have any idea on how to solve this? I really prefer the geom='point' option.
PDFs are vector based - so every single point on your chart has to be loaded individually. This produces a 'load-up' sort of effect on your PDF. My solution would be to save as a high DPI png/gif instead:
ggsave(file="xxx.png", dpi=400) #default is 300 which is probably sufficent
Tex to pdflatex (or AN Other) will find the file 'xxx' if you not forced an extension in your R to Tex conversion as the include statement will usually not mention an extension. You will need to make sure that the pdf is deleted from the your charts folders to ensure it doesn't get picked up in preference to the png.