plotMatrix: plotMatrix
In Umatrix: Visualization of Structures in High-Dimensional Data

Description Arguments Details Value References Examples

View source: R/plotMatrix.R

Draws a plot based of given Umatrix or Pmatrix.

`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

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

A 'ggplot' of a Matrix

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.

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

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