For some reason, when using ordihull and orditop to create a plot for my NMDS plot, I cannot for the life of me get it to be centered. I am using RStudio.
I have tried to reset the plot area using dev.off(), followed by plot.new() and using default values such as par(mfrow=c(1,1) par(mar=c(0,0,0,0)).
But here is an image of what my plot looks like using plot.new(), par(mar=c(10,10,10,10))
No matter what I put in par(mar), it is always cutting off my plot. I have no idea why this is happening or how to fix it.
Seems like when using ggplot2 (which is one the libraries I did load), the plot works by first running an empty plot such as plot(example_NMDS) without any other features, or running plot(example_NMDS, type="n") to set up the empty space first. Then run ordiplot. I think ordiplot(type="none") will also do the trick.
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 am experimenting with the investigate_var_importance in package of bartMachine
investigate_var_importance(bart_machine_cv, num_replicates_for_avg = 20)
It turns out that the generated graph is so big, especially the text label along with the x-axis. The default [R Graphics: Device 2(Active) cannot even hold the whole picture. How to change the font size and margin of this plot?
margin can be set by par(mar=c(bottomMargin, left, up, right))
see par to set that parameter
c(0,0,0,0) will not leave any space. You might not want this, as there wouldn't be any space for the axis.
par(oma=c(bottomMargin, left, up, right))
sets the outer margins of the plot
if you send the plot to a pdf, you can increase the size of the plot, which will be able to hold the whole plot i.e,
pdf('nameOfplot.pdf', 20, 6) ## opens a device, and produces a file much wider than longer
plot whater you want
dev.off() ## closes the device you have opened with pdf
if you play with those parameters you might be able to fit your plot
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