I am using tableGrob in R to create a .png image of a formatted table, for inclusion in a MS Word report. For small tables this works, but for larger ones they do not fit in the image. I haven't been able to find any parameters that allow me to either force it to fit automatically, or to manually control the height and width of the image window.
I would be very grateful if somebody could show me how to do this.
I am using R version 3.3.1, via Rstudio version 1.0.136, on Linux Mint on a 64-bit PC. R packages used include gridExtra, gridGraphics, gtable and png.
The table (tabsave) is a simple data frame with 34 rows and six columns, the first being chr and all the others num.
Here is what the output looks like. You can see how the table extends beyond both the upper and lower borders of the image:
Here is the relevant code
gtab<-tableGrob(tabsave,rows=NULL,cols=nm,theme = ttheme_default(base_size=10)) # gtab is the graphical version of the table, for printing
png('test.png')
grid.draw(gtab)
dev.off()
Thank you for any help you can provide.
The solution is to give width and height parameters to the png function. They both default to 480, in the default unit of pixels (px).
So I just changed
png('test.png')
to
png('test.png',height=1200)
I played around with the width and height parameters until it gave the coverage I needed.
When the plotting is to the interactive plot device, rather than to a file (ie not using a function like png) it's just a matter of first resizing the plot window so it's big enough.
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.
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
I have a very long time series of data to plot, and if I "zoom in" enough to see the interesting features, I can only look at a very small section of the data, and must replot every time I want to look at a different time window.
What I would like is a solution that gives me a graph with a horizontal scroll bar so I can browse around within the long time series.
My current preferred solution is gnuplot/aquaterm on OS X. It doesn't appear that this can do what I want - I can specify "set size 2.0,1.0" but this just causes the graph to spill over the window bounds, without causing a scroll bar to appear.
Can anybody recommend a solution that will do what I want - preferably with gnuplot, but any solution would do. I could of course write my own gnuplot gui terminal (or mess around with aquaterm), but I don't unfortunately have time for that!
Thanks for any suggestions.
Jonny
If you use an image terminal you can make it arbitrarily wide:
set terminal png size [width]x[height]
set output '[fname].png
Then open the output png file in an image viewer that scrolls.