Description Arguments Details Value References Examples

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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[1] "---- Esom Training Finished ----"
[1] "shift to point of highest density"
```

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