plotMatrix: plotMatrix

In Umatrix: Visualization of Structures in High-Dimensional Data

plotMatrix

Description

Draws a plot based of given Umatrix or Pmatrix.

Arguments

Matrix	Umatrix or Pmatrix to be plotted
BestMatches	Positions of BestmMtches to be plotted onto the Umatrix
Cls	Class identifier for the BestMatches
ClsColors	Vector of colors that will be used to colorize the different classes
ColorStyle	If "Umatrix" the colors of a Umatrix (Blue -> Green -> Brown -> White) will be used; If "Pmatrix" the colors of a Pmatrix (White -> Yellow -> Red) will be used
Toroid	Should the Umatrix be drawn 4times?
BmSize	Integer between 0.1 and 5, magnification factor of the drawn BestMatch circles
DrawLegend	If TRUE, a color legend will be drawn next to the plot
FixedRatio	If TRUE, the plot will be drawn with a fixed ratio of x and y axis
CutoutPol	Only draws the area within given polygon
Nrlevels	Number of height levels that will be used within the Umatrix
TransparentContours	Use half transparent contours. Looks better but is slow
Imx	Mask to cut out an island. Every value should be either 1 (stays in) or 0 (gets cut out)
Clean	If TRUE axis, margins, ... surrounding the Umatrix image will be removed
RemoveOcean	If TRUE, the surrounding blue area around an island will be reduced as much as possible (while still maintaining a rectangular form)
TransparentOcean	If TRUE, the surrounding blue area around an island will be transparent
Title	A title that will be drawn above the plot
BestMatchesLabels	Vector of strings corresponding to the order of BestMatches which will be drawn on the plot as labels
BestMatchesShape	Numeric value of Shape that will be used. Responds to the usual shapes of ggplot
MarkDuplicatedBestMatches	If TRUE, BestMatches that are shown more than once within an island, will be marked
YellowCircle	If TRUE, a yellow circle is drawn around Bestmatches to distinct them better from background

Details

The heightScale (nrlevels) is set at the proportion of the 1 percent quantile against the 99 percent quantile of the matrix values.

Value

A 'ggplot' of a Matrix

References

Thrun, M. C., Lerch, F., Loetsch, J., Ultsch, A.: Visualization and 3D Printing of Multivariate Data of Biomarkers, in Skala, V. (Ed.), International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision,Plzen, 2016.

Ultsch, A.: Maps for the visualization of high-dimensional data spaces, Proc. Workshop on Self organizing Maps (WSOM), pp. 225-230, Kyushu, Japan, 2003.

Siemon, H.P., Ultsch,A.: Kohonen Networks on Transputers: Implementation and Animation, in: Proceedings Intern. Neural Networks, Kluwer Academic Press, Paris, pp. 643-646, 1990.

Examples

data("Hepta")
e = esomTrain(Hepta$Data, Key = 1:nrow(Hepta$Data))
plotMatrix(e$Umatrix,e$BestMatches)

Umatrix documentation built on June 8, 2025, 12:03 p.m.