I'm using corrplot in R to plot the correlation matrrix. For some reason, the edges of the circles in the plot seems missing some pixels. The plot overall looks very rough. Please see the graph I plotted:
enter image description here
But the example I followed shows the plot is supposed to be like this:
enter image description here
My initial guess was dpi and scaling issue because I use a 4K display. I tried changing the resolution and size of the plots but it doesn't work.
Thank you so much for your help.
Related
What I would like to do is make a series of plots that combine an image with a scale that is related to the height of the image, but is multiplied by a factor.
So far I've been able to make a plot using the following code:
library(imager)
im <- load.image("ZAB17_4.png")
plot(im)
Image is attached here
But what I would like to do is to have the y-axis be scaled by a value:
pixel_size <- 0.0596
I would also get rid of the x-axis. (xaxt="n" doesn't seem to do the trick). Ideally, I would like the Y-axis to be directly adjacent to the image. I've been trying to poke around with scales in the plot function, but haven't found what I need to do this, but I'm sure there is a simple solution.
*Edited to add image. I should note that the goal is really just to add a scale to the image. The pixel size represents the size of each pixel in reality in mm. I basically want to add a ruler along the side of the image. Maybe r is not the best tool for this, but I plan to also plot data taken from the imaged object and plot it alongside.
Any help is appreciated.
I try to use R package - corrplot.
An example, i do this code:
M<-cor(mtcars)
corrplot(M, method="circle")
I get this image. It's ok, but if I want to look it inr my RStudio, i get this:
The image is shifted down, part of the characters are not visible. If there were more variables to correlate, it would be much worse. Maybe there are customizable parameters for image output and / or centering it?
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.
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).
These days I am extensively using R to scatter plots.
Most of the plotting is concerned with image processing,
Recently I was thinking of plotting the scatter plots over an image.
For example, I want something like this,
The background needs to be filled with my image. With a particular scale.
And I should be able to draw points (co-ordinates) on top of this image ...
Is this possible in R?
If not, do you guys know of any other tool that makes this easy ...
I'm not 100% sure what you have in mind, but I think first you want to load and plot an image in R. You can do that with the ReadImages package:
picture <- read.jpeg("avatar.jpg")
plot(picture)
Then you can do a scatter plot on top of it:
points(runif(50,0, 128), runif(50,0,128))
A step-by-step tutorial to this kind of plotting is in the R-wiki