Name of the output file of visual. visual is the tool of SOM_PAK which maps pattern to the codebook vectors of a self-organising map. The function reads files in the format created by visual.

Name of the SOM_PAK input file. This files contains all input patterns and class information for each pattern. som-plot only uses the last colums of the file; i.e. the class information for each pattern. The function reads files in the format that is used by SOM_PAK.

Many other arguments can be given to control the appearence of the plot:

‘col’, default colours for the classes of the dataset. Possible values include:

‘default value: NA.’ Colours are generated by rainbow()

‘vector’ of colour definitions

‘data frame’ with name of a class in column 1 and colour definitions in column 2.

If the number of defined colours is smaller then the number of classes in the dataset, colours for the remaining classes are generated by rainbow.

‘onlyDefCols’ default: FALSE; if TRUE, all undefined colours are replaced by white

‘edit.cols’ default: FALSE; if TRUE, a dialog box opens and allows editing of all color definitions

‘show.legend’ default: TRUE; defines if colour legend is displayed

‘legend.width’ default: 4; Width of legend

‘turn’ default: FALSE; swap X and Y axis

‘window.width’ default: NA; width of the window

‘window.height’ default: NA; height of the window

‘show.box’ default: TRUE; show frame around the plot

‘show.axis’ default: FALSE; show x and Y axis

‘scaleX’ default: NA; scale factor for X axis (overwrites new.xdim argument)

‘scaleY’ default: NA; scale factor for Y axis (overwrites new.ydim argument)

‘scale’ default: NA; scale factor for X and Y axis (overwrites other scale argument)

‘new.xdim’ default: NA; scale X axis to specified number of neurons

‘new.ydim’ default: NA; scale Y axis to specified number of neurons

‘show.counter.border’ default: 0.98 percentile as limit for the display of labels in the pie charts