Strange object in vector3d() graphic when using matlib + rgl

Question

I'm trying to plot 3-dimensional vectors (x, y, z coordinates) onto a 3D coordinate system in R like in the picture below. Ideally, I would then like to construct 3d kernel density plots, also like in the image below.

Ideal result of vector plot and 3d kernel density plot

I have a matrix containing ~100 rows and one column for each coordinate (x, y , z). Initially, I tried arrow3D() from the plot3D package but I find the perspective to be sub-par, it's rather difficult to discern directions of the arrows from one perspective in the final plot. Next I tried the rgl package which gives me interactivity - great. Minimal working example:

library(rgl)
library(matlib)

data2 <- data.frame(replicate(6,rnorm(100))) #sample data set for minimum working example

colnames(data2) <- c("x_target", "y_target", "z_target", "x_start", "y_start", "z_start")

x1 <- data2$x_target - data2$x_start
y1 <- data2$y_target - data2$y_start
z1 <- data2$z_target - data2$z_start

vec <- (diag(6,3))     # coordinates for x, y and z axis
rownames(vec) <- c("X", "Y", "Z")   # labels for x, y and z axis

z <- as.matrix((data.frame(x=x1, y=y1, z=z1)))

open3d()

vectors3d(vec, color=c(rep("black",3)), lwd=2, radius=1/25)
vectors3d(X=z, headlength=1/25)

(due to the random numbers generator the strange looking rods appear at different coordinates, not exactly like in the image i link to below)

The result of the code above is a version of the image link below. One set of coordinates produces a very strange looking more like rod object which is far longer then the coordinates would produce. If I plot the vectors individually, no such object is created. Anyone have any ideas why this happens? Also, if anyone has a tool (doesn't have to be R), that can create a 3D vector plot like in the first image, I'd be grateful. I find it to be very complicated in R, but I'm definitely a beginner.

Strange object to the right (long red rod that doesn't look like an arrow at all)

Thank you!

Where did you find the vectors3d function? It's not in rgl. And more generally: we can't reproduce your example, because we don't have x1, y1, or z1. Please post a reproducible example. — user2554330
I apologize. It's from the matlib package. I will provide x1, y1, z1 right away! The code above now works on my system. — Linus Köster

user2554330 user2554330 · Accepted Answer · 2019-04-16T01:15:59

This is due to a bug in the matlib package, fixed in verson 0.9.2 of that package. I think you need to install it from Github instead of CRAN to get the bug fix:

devtools::install_github("friendly/matlib")

BTW, if you are using random numbers in a reproducible example, you can make it perfectly reproducible by something like

set.seed(123)

at the start (or some number other than 123). I saw reproducible problems with your example for set.seed(4).

Strange object in vector3d() graphic when using matlib + rgl

1 Answers