gem {RepeatedHighDim} | R Documentation |
Plots a gemstone to an interactive graphics device
Description
Plots a gemstone to an interactive graphics device.
Usage
gem(coords, hull, clr)
Arguments
coords |
Matrix with coordinates of the grid or of data
points that belong to the gemstone, calculated by either
|
hull |
Matrix with indices of triangles that cover a convex hull arround the gemstone. Each row represents one triangle and the indices refer to the rows of coords. |
clr |
Specifies the color of the gemstone. |
Details
Only applicable to 3-dimensional data sets. Transparent colors are recommended for outer gemstone of the gemplot. Further graphical parameters can be set using material3d() of the rgl-package.
Author(s)
Jochen Kruppa, Klaus Jung
References
Rousseeuw, P. J., Ruts, I., & Tukey, J. W. (1999). The bagplot: a bivariate boxplot. The American Statistician, 53(4), 382-387. doi:10.1080/00031305.1999.10474494
Kruppa, J., & Jung, K. (2017). Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. BMC bioinformatics, 18(1), 1-10. https://link.springer.com/article/10.1186/s12859-017-1645-5
See Also
For more information, please refer to the package's documentation and the tutorial: https://software.klausjung-lab.de/.
Examples
## Attention: calculation is currently time-consuming.
## Not run:
# Two 3-dimensional example data sets D1 and D2
n <- 200
x1 <- rnorm(n, 0, 1)
y1 <- rnorm(n, 0, 1)
z1 <- rnorm(n, 0, 1)
D1 <- data.frame(cbind(x1, y1, z1))
x2 <- rnorm(n, 1, 1)
y2 <- rnorm(n, 1, 1)
z2 <- rnorm(n, 1, 1)
D2 <- data.frame(cbind(x2, y2, z2))
colnames(D1) <- c("x", "y", "z")
colnames(D2) <- c("x", "y", "z")
# Placing outliers in D1 and D2
D1[17,] = c(4, 5, 6)
D2[99,] = -c(3, 4, 5)
# Grid size and graphic parameters
grid.size <- 20
red <- rgb(200, 100, 100, alpha = 100, maxColorValue = 255)
blue <- rgb(100, 100, 200, alpha = 100, maxColorValue = 255)
yel <- rgb(255, 255, 102, alpha = 100, maxColorValue = 255)
white <- rgb(255, 255, 255, alpha = 100, maxColorValue = 255)
require(rgl)
material3d(color=c(red, blue, yel, white),
alpha=c(0.5, 0.5, 0.5, 0.5), smooth=FALSE, specular="black")
# Calucation and visualization of gemplot for D1
G <- gridfun(D1, grid.size=20)
G$H <- hldepth(D1, G, verbose=TRUE)
dm <- depmed(G)
B <- bag(D1, G)
L <- loop(D1, B, dm=dm)
bg3d(color = "gray39" )
points3d(D1[L$outliers==0,1], D1[L$outliers==0,2], D1[L$outliers==0,3], col="green")
text3d(D1[L$outliers==1,1], D1[L$outliers==1,2], D1[L$outliers==1,3],
as.character(which(L$outliers==1)), col=yel)
spheres3d(dm[1], dm[2], dm[3], col=yel, radius=0.1)
material3d(1,alpha=0.4)
gem(B$coords, B$hull, red)
gem(L$coords.loop, L$hull.loop, red)
axes3d(col="white")
# Calucation and visualization of gemplot for D2
G <- gridfun(D2, grid.size=20)
G$H <- hldepth(D2, G, verbose=TRUE)
dm <- depmed(G)
B <- bag(D2, G)
L <- loop(D2, B, dm=dm)
points3d(D2[L$outliers==0,1], D2[L$outliers==0,2], D2[L$outliers==0,3], col="green")
text3d(D2[L$outliers==1,1], D2[L$outliers==1,2], D2[L$outliers==1,3],
as.character(which(L$outliers==1)), col=yel)
spheres3d(dm[1], dm[2], dm[3], col=yel, radius=0.1)
gem(B$coords, B$hull, blue)
gem(L$coords.loop, L$hull.loop, blue)
# Example of outlier detection with four principal components.
# Attention: calculation is currently time-consuming.
set.seed(123)
n <- 200
x1 <- rnorm(n, 0, 1)
x2 <- rnorm(n, 0, 1)
x3 <- rnorm(n, 0, 1)
x4 <- rnorm(n, 0, 1)
D <- data.frame(cbind(x1, x2, x3, x4))
D[67,] = c(7, 0, 0, 0)
date()
G = gridfun(D, 20, 4)
G$H = hldepth(D, G, verbose=TRUE)
dm = depmed(G)
B = bag(D, G)
L = loop(D, B, dm=dm)
which(L$outliers==1)
date()
## End(Not run)