plotMatrix: plotMatrix

Description Arguments Details Value References Examples

View source: R/plotMatrix.R

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

1
2
3
data("Hepta")
e = esomTrain(Hepta$Data, Key = 1:nrow(Hepta$Data))
plotMatrix(e$Umatrix,e$BestMatches)

Example output

[1] "Epoch: 1 started"
[1] "Epoch: 2 started"
[1] "Epoch: 3 started"
[1] "Epoch: 4 started"
[1] "Epoch: 5 started"
[1] "Epoch: 6 started"
[1] "Epoch: 7 started"
[1] "Epoch: 8 started"
[1] "Epoch: 9 started"
[1] "Epoch: 10 started"
[1] "Epoch: 11 started"
[1] "Epoch: 12 started"
[1] "Epoch: 13 started"
[1] "Epoch: 14 started"
[1] "Epoch: 15 started"
[1] "Epoch: 16 started"
[1] "Epoch: 17 started"
[1] "Epoch: 18 started"
[1] "Epoch: 19 started"
[1] "Epoch: 20 started"
[1] "Epoch: 21 started"
[1] "Epoch: 22 started"
[1] "Epoch: 23 started"
[1] "Epoch: 24 started"
[1] "---- Esom Training Finished ----"
[1] "shift to point of highest density"

Umatrix documentation built on Feb. 12, 2020, 5:58 p.m.