As a beginner on R I manage to produce correct relational graphs thanks to R. They are about correct in the visualization space but of very bad quality when I export them in PDF or in JPEG / PNG. The image is not centered, a part of the legend is missing, the graph is very small or blurred etc.
How do you proceed for the export?
Thanks in advance!
I am looking for the right handling or settings to export the graph visualizations produced in R?
I understood that I had to set up the viewer space but via the code but have no idea how to do it...
Here an example how to write a plot to a PNG file. The plot "commands" are embedded in png(....)and dev.off(). Several options are available to configure size and resolution.
png("myfile.png", width=1600, height=1200, res=300) # good for LaTeX or Word
#png("myfile.png", width=800, height=600, res=150) # good for Powerpoint or Impress
plot(iris$Sepal.Length, iris$Petal.Length)
dev.off()
Some hints:
width and height are given in pixels
res influences nominal resolution and font size (play with it)
use at least 300 dpi (dots per inch). For centimeters, the number of pixels = 300/2.54 * width in cm
professionals use 600 or even 1200 pixels per inch, but then .docx and .pptx files will dramatically increase
1600 x 1200px is good for 13.3 x 10 cm size in the printed document
If you work with LaTeX, it is in most cases better to use PDF for the figures. Another very good idea is to use Markdown for the text. Then, figures are automatically embedded.
I'm saving a plot in R that I made with ComplexHeatmap. However, when I save it as a PDF, I could see that there are horizontal lines in the annotation bar. I don't have this issue when I save it as a png file but the plot is blurry. How can I save my plot so that it is clear and the lines don't appear?
In R, the resolution of a plot saved as a PDF is related to the size of the PDF page. You can increase the size, and therefore the resolution, by adding to your code this:
pdf(width = 32, height = 18 , onefile = T)
Followed by the plotting code, and ending with dev.off().
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 created a plot from a very large vector (magnitude of 10^7). The problem with the usual way of saving the plot as a pdf file is that the pdf file comes out as a very large file of around 10MB. I don't want such a large size for a simple time series plot. How do I save the plot such that the size is small enough to be at most 100kilobytes?
baptiste is on the right track with their suggestion of png for a nice raster type plot. In contrast to Jdbaba's suggestion of copying the open device, I suggest that you make a call to the png()device directly. This will save a lot of time in that you won't have to load the plot in a separate device window first, which can take a long time to load if the data set is large.
Example
#plotting of 1e+06 points
x <- rnorm(1000000)
y <- rnorm(1000000)
png("myplot.png", width=4, height=4, units="in", res=300)
par(mar=c(4,4,1,1))
plot(x,y,col=rgb(0,0,0,0.03), pch=".", cex=2)
dev.off() #only 129kb in size
see ?png for other settings of the png device.
If you want to plot the png file use the following command:
dev.copy(png,"myfile.png",width=8,height=6,units="in",res=100)
dev.off()
you can change res value to higher value if you want to output high quality graphs.
If you want to save the file as pdf use the following command:
pdf("myfile.pdf",width=8,height=6)
dev.off()
Remember to change the width and height values as needed.
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