I have a problem changing the text size of a 3d plot I generated with the package rgl. Everything works fine, but I can't effectively change the cex properties of an 3d object. I run R 2.14.1 (2011-12-22) under 64bit Ubuntu 10.04 LTS (2.6.32-37-generic). As an example see the following code (I found on Stack Overflow):
library(rgl)
set.seed(1001)
n <- 20
text3d(runif(n),runif(n),runif(n),LETTERS[1:n],cex=seq(0.5,5,length=n))
The letters have all the same size when I plot them.
Any help is highly appreciated! Best Regards.
Frieder Schillinger
Weird. It works for me on Ubuntu 10.04 (rgl 0.92.829) [this is my code, I think]. Can you tell us your rgl version? By "plot" do you mean rendering the picture on the screen, or producing PostScript output? This was fixed in the most recent (0.92.829) version:
> news(grepl("text",Text),package="rgl")
Changes in version 0.92.829:
o rgl.postscript() now adjusts the size of text following the cex setting.
The font and family settings are still ignored.
o Transparency in material textures was not always rendered properly.
?text3d
There is no cex argument. You should be using "scale".
Related
Hi guys,
I have set up a new conda R-environment (on my ubuntu 20.04) and oddly, the output of the base plot function does not show symbols on the axes or axis labels but little squares with numbers instead (see attached picture).
When I use the plot function in an R-Markdown code chunk and export it as PDF, the plot is displayed correctly. However, in RStudio or when exporting the Rmd to html, the symbols appear like in the picture.
I realize this could have to do with the encoding, but don't know how to solve it. Has anyone encountered this problem before or can give me advice how to troubleshoot it?
Many thanks in advance!
Simply adding the package r-cairodevice to my R environment solved the problem.
Saving the output of one of R's built-in examples for the filled.contour function to PDF:
pdf('test.pdf')
require("grDevices")
filled.contour(volcano, asp = 1)
dev.off()
produces a discretised result (see below). Is there any way to fix this? System info:
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Edit after the accepted answer:
The problem is actually reported in the documentation of the pdf function:
If you see problems with PDF output, do remember that the
problem is much more likely to be in your viewer than in R ...
Symptoms for which the viewer has been at fault are apparent
grids on image plots ...
Unfortunately the default viewers on most Linux and macOS
systems have these problems, and no obvious way to turn off
graphics anti-aliasing.
It's an odd place to document the problem because the subdivision into rectangular segments is clearly caused by filled.contour and not by pdf. Otherwise ggplot2's output would also suffer from the same issue.
That is likely a result of antialiasing: when you display the image, it draws squares one at a time. As they are being drawn, the edge is a mix of the square colours and the white background, so it is drawn lighter.
Unfortunately, this isn't something that's really under your control. It's the PDF previewer that is introducing the artifacts. See this page https://codedocean.wordpress.com/2014/02/03/anti-aliasing-and-image-plots/ for a discussion.
The recommendation there worked for me: use the png() device with type = "cairo". This gives bitmapped output rather than the vector output of a pdf().
png('test.png',type="cairo")
filled.contour(volcano, asp = 1)
dev.off()
Edited to add:
I don't think you can do better with filled.contour, but if you are willing to switch to ggplot2 graphics you can. When it draws filled contours it appears to do it using polygons, not the image style plot that filled.contour uses. This still shows the same antialiasing bugs in the previewer, but now the lines appear along the borders between colours, which is much less irritating. For example:
df <- data.frame(x = as.numeric(row(volcano)-1)/(nrow(volcano)-1),
y = as.numeric(col(volcano)-1)/(ncol(volcano)-1),
z = as.numeric(volcano))
pdf('test.pdf')
library(ggplot2)
ggplot(df, aes(x=x, y=y, z=z)) +
geom_contour_filled()
dev.off()
I don't know how to get the same palette as filled.contour uses, i.e. function(n) hcl.colors(n, "YlOrRd", rev = TRUE). Maybe someone else can show us in a comment.
Sometimes, R draws white lines across an image plot for no apparent reason. Other plotting commands like lines() or contour() are not affected. This example is with x11, but it has happened with png() as well.
It can be fixed by changing the figure geometry. For example, a vertical white line can be eliminated by changing the width of the plot. But, this is not a real solution to the problem: many of my codes need to create publication-quality figures in scripts without supervision, often in packages I distribute to others.
Has anyone else encountered this? Does anyone know how to fix it? I'm using Ubuntu 16.04 64-bit with R version 3.3.1 (2016-06-21) -- "Bug in Your Hair", but have had this problem for years with many versions of R.
Here's an example code and image.
x = 4 * 0:1250
y = 4 * 0:1325
Z = matrix(rnorm(1251*1326), 1251)
image(x, y, Z)
Try setting the logical useRaster option within the image function. As in:
x = 4 * 0:1250
y = 4 * 0:1325
Z = matrix(rnorm(1251*1326), 1251)
image(x, y, Z, useRaster = TRUE)
According to the details within ?image(),
Images for large ‘z’ on a regular grid are rendered more efficiently with 'useRaster = TRUE’ and can prevent rare anti-aliasing artifacts
See the man page for the full description.
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'm trying to generate a 3d scatterplot using rgl. It looks great on my screen, but whenever I export it as a PDF (or any other postscript format) it completely ignores any size specifications I use.
(I'm running RGui v.2.15.1 and rgl v.0.92.892 on a Macbook under Mountain Lion.)
For example:
library(rgl)
set.seed(1982)
points3d(runif(5),runif(5),runif(5), size=20)
# points look huge
rgl.postscript('testplot.pdf', fmt='pdf')
# points look tiny
Does anyone have an idea for a way to get this to work? The resolution of the images I get using rgl.snapshot don't look so good, and I would really like to get a vector image for this plot.
Also, I followed this thread and I got text to resize just fine, but not points. So I thought one way to work around this would be to plot my points as text using a circle as my character, but I couldn't get rgl to accept symbols or expressions either...
Confirmed on Windows, look like some paper size scaling problem. You might try
spheres3d(runif(5),runif(5),runif(5),radius=0.1)
as a workaround if you can live with real 3d.