Error in plot.new() : figure margins too large in R

Question

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)

Answer 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!

Answer 2

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:

1. 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.

2. 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

3. 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)

Answer 3

If you get this message in RStudio, clicking the 'broomstick' figure "Clear All Plots" in Plots tab and trying plot() again may work.

Answer 4

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() 

Answer 5

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

Answer 6

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.

Answer 7

Just zoom this area if you use RStudio.

Answer 8

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.

Answer 9

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

Answer 10

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...

Answer 11

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)
    ```

Answer 12

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.

Answer 13

I have just use the Clear all plots then again give the plot command and it was helpfull

Answer 14

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.