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
Related
I'm interesting in adjusting margins for R plots. I use R Studio on MacOS, run on a 2013 intel CPU Macbook pro.
Here is the data I used for generating the plot:
spins <- runif(50, min = 0, max = 50)
Here is the code I used to generate the plot:
hist(spins)
Here is the results of the console:
> hist(spins)
Error in plot.new() : figure margins too large
Here are my questions:
How do I find out the current margins of this specific plot?
How do I modify the margins for this specific plot?
Is there a method to modify the margins for plots in general (e..g., Can I use 1 set of code to find the margins of the object and then use a second set of code to modify the margins so it will display in the plots area)?
Is there code I can use to automatically adjust the margins of the plots so that the desired plot displays every time?
The par function can be used to see the size of current margins and to set margin sizes (plus a whole bunch of other things).
Running par(c("mar", "mai")) will report the current margins (starting at bottom and going clockwise) in lines of text (mar) and inches (mai).
You can then set the margins using code like: par(mar=c(2,2,2,0)) or par(mai=rep(0.4, 4)).
But the problem is probably that you have made the plots pane in RStudio too small in at least one dimension, so when the hist function tries to create the plot there is not enough room for the plot and margin information. Try dragging the appropriate dividers within RStudio to make the plot panel larger then try your code again. Another option is to run the command dev.new() which will open a new window for the plots (using the default for your OS) and by default send the plot to that new window instead of the plot pane in RStudio.
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)
My goal is to read an image file in either the PNG or JPEG format and plot various data over said image and save it to disk.
I also want the image to take up all available space in the produced plot, no axes or labels or anything. I'm a bit concerned that this might be relevant to my problem.
Code example
Below is my current code that currently only tries to output the same image as you put in. Later I plan on plotting data points corresponding to coordinates over the image. I've used some sample code found here in order to remove the axes and be able to have the image in the background of the plot.
library(jpeg)
library(grid)
img <- readJPEG(system.file("img", "Rlogo.jpg", package="jpeg"),native=TRUE)
jpeg(filename = "Rlogo-2.jpg", width=100,height=76, quality = 100,res=299)
op<-par(mar=rep(0,4))
plot(0:100,type="n", axes="FALSE",ann="FALSE")
lim <- par()
rasterImage(img, lim$usr[1], lim$usr[3], lim$usr[2], lim$usr[4])
dev.off()
Example output
This is an example output of my above code in a comparison with the original image:
The image to the left is the original and the right one is the modified one. As you can see it seems as if the image I read and plot somehow is smaller than the original image and when saved to the original dimensions it appears blurred.
I've been pulling my hair over this one for hours and I don't seem to get anywhere. This is my first attempt to plot data over images and I'm aware of my lack of knowledge about how R represents images and I've mostly been using the basic graphics to do relatively simple plots before.
I'm currently considering doing this in Python instead but I'm afraid that'll come back and bite me when it comes to the actual plotting of the data.
I run R version 3.1.0 on x86_64 running Windows 7.
Just to summarize, since you already found the culprit, there are two issues present here:
Firstly, the blurring appears to be caused by the jpeg device on Windows. There is no such problem on Ubuntu Linux and it disappears if you use the Cairo-device instead, as you did already discover. Cairo-devices are great for pdf:s too since they embed all the fonts etc. making the figure look the same across platforms.
Secondly, R adds 4% extra margin to the x and y axes by default to prevent graphics from being chopped off near the edge of the plot area. It can be corrected by setting xaxs="i" and yaxs="i".
par(mfrow=1:2)
plot(1:5, 1:5) # Left
plot(1:5, 1:5, xaxs="i", yaxs="i") # Right
In your case the difference is subtle but still would cause everything to be slightly misaligned.
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.
In R, I met a running error as follows:
> png("p3_sa_para.png", 4, 2)
> par(mfrow=c(1,2))
> plot(c(1:10), ylab="Beta",xlab="Iteration")
Error in plot.new() : figure margins too large
> plot(c(1:10), ylab="Gamma",xlab="Iteration")
Error in plot.new() : figure margins too large
> dev.off()
X11cairo
2
I have already made the image size small to be 4 by 2, why it still complains "figure margins too large"? How can I solve this problem with png?
It is strange that if I change png to pdf, then it will work. I also wonder why?
Thanks and regards!
The png() function uses pixels not inches, so try something like
png("p3_sa_para.png", 640, 480)
And to answer your second question, yes, pdf() uses inches because a vector-graphics format has no notion of pixels. The help(png) and help(pdf) functions are your friends.
The problem can simply arise from using a certain IDE. I was using Rstudio, and I got a slew of errors. My exact same code worked fine in the console.
Even I was getting the error on R-Studio, while the plot was appearing fine on the console. A simple restart of RStudio solved the problem! Having said that, RStudio's support page suggests that resetting graphics device dev.off() may help. http://support.rstudio.org/help/kb/troubleshooting/problem-with-plots-or-graphics-device
This is a common issue for plotting specially when you are using IDE which has a place for generating and showing you the plot, thought it's a general issue and there is a logic behind it:
when you tell R to plot something, R first look at the data and then looks at the area it has at it's disposal so that it cal do the plotting.
The png() and similar commands:
In your case you gave the plot a 4 by 2 pixel area to plot it, so you can solve it by increasing the area in a size that can fit your plot. (as Dirk Eddelbuettel mentioned)
In case of IDE
This is much simpler in most cases, just increase the plotting area by dragging the margins and then re-run your code (close any par() if you have any opened before and create new one)