When I add a legend to my R plot (using the legend() function), then it works in Rstudio, but when I export the plot as a PDF with a different size, then sometimes the text inside the legend is larger than the legend box itself.
What is going on here and how do I fix it?
If I export the image with a larger width, then the legend box becomes larger too and manages to contain its text, but this is silly: I want the legend box and its text to automatically adjust to whatever width I choose, no matter how small it is.
And please don't recommend ggplot2.
As #Gregor said - you should use pdf(). I am merely adding his suggestion as an answer. Your code would be something like this:
pdf("picture.pdf", width=6, height=6)
plot(...)
legend(...)
dev.off()
Where pdf() opens a new device for plotting (of course you have to set file name as well as dimensions according to your needs), and dev.off() closes the device writing everything to a file.
I am not sure what causes the issue with legend in R-studio. But on my machine I noticed that legends sometimes have issues with updating after resizing the device. Probably this is something related.
I am running R in jupyter, but I am running across some issues with plotting. Specifically whenever I plot the returned plotting window takes up the entire screen. I tried changing the dimension of the plot in R with par(pin=c(1,1)) etc... and it shrunk the actual image of the plot, but the cell width the images is in still takes up the entire screen. I can zoom out in my browser, but then I can't see my lines of code.
Code:
x <- runif(100)
hist(x)
Any suggestions on how to fix this would be appreciated. Thanks.
P.S. I would post an image, but I just created this account and need at least 10 rep points to post images
Answer:
I was able to change the options with the code below so my plots looked a little bit more reasonable
options(repr.plot.height=3)
options(repr.plot.width=3)
I have a long time series of 10000 observations that I want to visualize. The problem is, if I just plot it normally the time-dimension will be squished and none of the fine detail of the time-series that I want to visualize will be apparent. For example:
plot((sin(1:10000/100)+rnorm(10000)/5),type='l')
What I would like is to somehow plot the following together side by side in one gigantically long plot without using par(mfrow=c(1,100)). I then want to export this very wide plot and simply scroll across to vizualise the whole series.
plot((sin(1:10000/100)+rnorm(10000)/5)[1:100],type='l')
plot((sin(1:10000/100)+rnorm(10000)/5)[101:200],type='l')
plot((sin(1:10000/100)+rnorm(10000)/5)[201:300],type='l')
.....
Eventually I would like to have 3 or 4 of these gigantically wide plots on top of each other with a par(mfrow=c(4,1)).
I know that the answer has something to do with the pin setting in par, but I keep getting Error in plot.new() : plot region too large. I'm guessing this has something to do with the interaction of pin with the other par parameters
Bonus points are awarded if we can get the pixel height and width exactly right. It is preferable that the plot doesn't skip random pixels due to the export sizing being imperfect.
Further bonus points if the image can be encoded in a .html. and viewed this way
An alternative that you might consider is svg, which will produce something of better quality than png/jpeg in any case.
Something like
svg(width = 2000, height = 7)
par(mfrow=c(4,1), mar = c(4, 4, 0, 2))
for (i in 1:4){
plot((sin(1:10000/100)+rnorm(10000)/5),type='l',
bty = "l", xaxs = "i")
}
dev.off()
will produce a very wide plot, just over 1MB in size, which renders quite nicely in Chrome.
Note the width and height are in inches here.
P.S. svg also offers the potential for interactive graphics. Just seen a nice example allowing the user to select a region of a long time series to zoom in on, see Figure 22 in Dynamic and Interactive R Graphics for the Web: The gridSVG Package, a draft paper by Paul Murrell and Simon Potter.
It could be a Cairo-specific problem, or it could be a lack of RAM on your machine. The following code works fine for me on a Windows 7 machine with 8GB RAM.
png("wide.png", width = 1e5, height = 500)
plot((sin(1:10000/100)+rnorm(10000)/5),type='l')
dev.off()
If I change the width to 1e6 pixels, then R successfully creates the file (it took about a minute), but no image viewing software that I have available can display an image that large.
I would go on some alternative route. First of all, what exactly is the point of viewing the entire plot at hi-res? If you're searching for some sort of anomalies or irregularities, well, that's what data processing is for :-) . Think about something like finding allx > 3sigma, or doing an FFT, etc.
Next, if you really want to examine the whole thing by eye, how about writing some R-TclTK code or using dynamicGraph or iplots or zoom to produce an interactive graph that you can scroll thru "live."
ETA: IIRC RStudio has tools for interactive graph scrolling and zoom as well.
I'm trying to generate a 3d scatterplot using rgl. It looks great on my screen, but whenever I export it as a PDF (or any other postscript format) it completely ignores any size specifications I use.
(I'm running RGui v.2.15.1 and rgl v.0.92.892 on a Macbook under Mountain Lion.)
For example:
library(rgl)
set.seed(1982)
points3d(runif(5),runif(5),runif(5), size=20)
# points look huge
rgl.postscript('testplot.pdf', fmt='pdf')
# points look tiny
Does anyone have an idea for a way to get this to work? The resolution of the images I get using rgl.snapshot don't look so good, and I would really like to get a vector image for this plot.
Also, I followed this thread and I got text to resize just fine, but not points. So I thought one way to work around this would be to plot my points as text using a circle as my character, but I couldn't get rgl to accept symbols or expressions either...
Confirmed on Windows, look like some paper size scaling problem. You might try
spheres3d(runif(5),runif(5),runif(5),radius=0.1)
as a workaround if you can live with real 3d.
I'm new to R but I've made numerous correlation plots with smaller data sets. However, when I try to plot a large dataset (2gb+), I can produce the plot just fine, but the legend doesn't show up. Any advice? or alternatives?
library(gplots)
r.cor <- cor(r)
layout(matrix(c(1,1,1,1,1,1,1,1,2,2), 5, 2, byrow = TRUE))
par(oma=c(5,7,1,1))
cx <- rev(colorpanel(25,"yellow","black","blue"))
leg <- seq(min(r.cor,na.rm=T),max(r.cor,na.rm=T),length=10)
image(r.cor,main="Correlation plot Normal/Tumor data",axes=F,col=cx)
axis(1, at=seq(0,1,length=ncol(r.cor)), labels=dimnames(r.cor)[[2]],
cex.axis=0.9,las=2)
axis(2,at=seq(0,1,length=ncol(r.cor)), labels=dimnames(r.cor)[[2]],
cex.axis=0.9,las=2)
image(as.matrix(leg),col=cx,axes=T)
Error in plot.new() : figure margins too large
tmp <- round(leg,2)
axis(1,at=seq(0,1,length=length(leg)), labels=tmp,cex.axis=1)
This error can occur in Rstudio simply because your "Plots" pane is just barely too small. Try zooming your "Files, Plots, Packages, Help, Viewer" and see if it helps!
The problem is that the small figure region 2 created by your layout() call is not sufficiently large enough to contain just the default margins, let alone a plot.
More generally, you get this error if the size of the plotting region on the device is not large enough to actually do any plotting. For the OP's case the issue was having too small a plotting device to contain all the subplots and their margins and leave a large enough plotting region to draw in.
RStudio users can encounter this error if the Plot tab is too small to leave enough room to contain the margins, plotting region etc. This is because the physical size of that pane is the size of the graphics device. These are not independent issues; the plot pane in RStudio is just another plotting device, like png(), pdf(), windows(), and X11().
Solutions include:
reducing the size of the margins; this might help especially if you are trying, as in the case of the OP, to draw several plots on the same device.
increasing the physical dimensions of the device, either in the call to the device (e.g. png(), pdf(), etc) or by resizing the window / pane containing the device
reducing the size of text on the plot as that can control the size of margins etc.
Reduce the size of the margins
Before the line causing the problem try:
par(mar = rep(2, 4))
then plot the second image
image(as.matrix(leg),col=cx,axes=T)
You'll need to play around with the size of the margins on the par() call I show to get this right.
Increase the size of the device
You may also need to increase the size of the actual device onto which you are plotting.
A final tip, save the par() defaults before changing them, so change your existing par() call to:
op <- par(oma=c(5,7,1,1))
then at the end of plotting do
par(op)
If you get this message in RStudio, clicking the 'broomstick' figure "Clear All Plots" in Plots tab and trying plot() again may work.
This sometimes happen in RStudio. In order to solve it you can attempt to plot to an external window (Windows-only):
windows() ## create window to plot your file
## ... your plotting code here ...
dev.off()
I got this error in R Studio, and was simply fixed by making the sidebar bigger by clicking and dragging on its edge from right to left.
Picture here: https://janac.medium.com/error-in-plot-new-figure-margins-too-large-in-r-214621b4b2af
Check if your object is a list or a vector. To do this, type is.list(yourobject). If this is true, try renaming it x<-unlist(yourobject). This will make it into a vector you can plot.
Just zoom this area if you use RStudio.
I found this error today. Initially, I was trying to output it to a .jpeg file with low width and height.
jpeg("method1_test.jpg", width=900, height=900, res=40)
Later I increased the width and height to:
jpeg("method1_test.jpg", width=1900, height=1900, res=40)
The error was not there. :)
You can also play with the resolution, if the resolution is high, you need more width and height.
I had this error when I was trying to plot high dimensional data. If that's what is going on with you, try multidimensional scaling: http://www.statmethods.net/advstats/mds.html
I struggled with this error for weeks (using RStudio). I tried moving the plot window bigger and smaller, but that did not consistently help. When I moved (dragged) the application to my bigger monitor, the problem disappeared! I was stunned... so many wasted hours... I knew my code was correct...
If margin is low, then it is always better to start with new plotting device:
dev.new()
# plot()
# save your plot
dev.off()
You will never get margin error, unless you plot something large which can not be accommodated.
RStudio Plots canvas is limiting the plot width and heights. However if you make your plot from Rmarkdown code chunk, it works without canvas field limitation because plotting area set according to the paper size.
For instance:
```{r}
#inside of code chunk in Rmarkdown
grid <- par(mfrow=c(4, 5))
plot(faithful, main="Faithful eruptions")
plot(large.islands, main="Islands", ylab="Area")
...
par(grid)
```
I found the same error today. I have tried the "Clear all Plots" button, but it was giving me the same error. Then this trick worked for me,
Try to increase the plot area by dragging. It will help you for sure.
I have just use the Clear all plots then again give the plot command and it was helpfull