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 am trying make a pyramid plot with R. The I found a example code in the internet that does what I want. The problem is that I am not working with small numbers as in the example. My plot has values of 3,000,000 to 12,000,000 but only 10 bars per side. Never the less it takes for ever create the plot with the larger numbers and output pdf file is about 800mb of size.
pyramid.plot(x,y,labels=groups,main="Performance",lxcol=mcol,rxcol=fcol,gap=0.5,show.values=TRUE)
Why is the performance so bad? Shouldn't get scaled automatically?
Update:
pdf(file='figure1.pdf')
library(plotrix)
x <-c(3105000,3400001,4168780,2842764,3543116,4224601,4222222,6432105,9222222,12345596)
y <-c(3105000,3400001,4168780,2842764,3543116,4224601,4222222,6432105,9222222,12345596)
groups <-c("g1","g2","g3","g4","g5","g6","g7","g8","g9","g11")
pyramid.plot(x,y,labels=groups,main="Performance",gap=0.5,show.values=TRUE)
dev.off()
Both the export to pdf as well as the plotting screen takes multiple minutes.
Internally, pyramid.plot is trying to do some stuff to finagle the axes accounting for the gap in the middle: if you do debug(pyramid.plot) and step through line-by-line you find where the problem is:
if (is.null(laxlab)) {
laxlab <- seq(xlim[1] - gap, 0, by = -1)
axis(1, at = -xlim[1]:-gap, labels = laxlab)
}
in other words, pyramid.plot is trying to make an axis with ticks every 1 (!) unit.
Something like this works OK:
pyramid.plot(x,y,labels=groups,
main="Performance",gap=5e5,show.values=TRUE,
laxlab=seq(0,1e7,by=1e6),raxlab=seq(0,1e7,by=1e6))
there are a few other vestiges of the fact that pyramid.plot was designed for demographic plots ... you might write to the package maintainer and ask him to think about generalizing the design of the axes a little bit ...
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
When plotting oscillations in R, e.g., using the package desolve,
df1 <-function(t,y,mu)( list(c(y[2],mu*y[1]^3-y[1]+0.005*cos(t))))
library (deSolve)
yini<-c(y1=0,y2=0)
df2 <-ode(y=yini,func=df1, times=0:520,parms=0.1667)
plot(df2,type="l",which="y1",ylab="Displacement",xlab="Time", main="")
I get raggedy plots such as:
instead of a smooth plot (not done in R) such as:
Does anyone know of a way to obtain a smoother plot in R instead of a raggedy one when displaying oscillations? Note that it is not just a matter of the difference in scale and I am not looking for a smoothing filter.
Thanks,
I generated your plot in R and exported it as PDF. I zoomed in on it and it's quite lovely. I can't see the problem you're talking about there. Therefore, there are some scaling issues or something with a raster format that are causing the issue. Perhaps you're pasting into Word and that's giving you a raster image that's bad. The plot that R is making, at a logical level, is great in spite of the one you posted. It's even better than the comparison plot you put up.
It's possible that you're generating the plot in a raster format and not setting a high enough resolution and size. Try tiff('filname', 1200, 1200, 300) for a good raster image of it. I did notice that when exporting to raster formats it was easy to make your plot into a fine mess with default png or jpg settings that would just smear things.
Maybe you really wanted to sample in your function at a higher resolution, something not done in the comparison plot. If that's the case then it's relatively easy. Change 0:520 to seq(0, 520, 0.1). That's an even nicer plot, as shown below (much better than shown as PDF, EPS, or SVG).