SOM Toolbox | Online documentation | http://www.cis.hut.fi/projects/somtoolbox/ |

Shows basic visualizations of SOM: component planes, unified distance matrices as well as empty planes and fixed color planes.

h = som_show(sMap) h = som_show(sMap, 'argID', value, ...)

This function is used for basic visualization of the SOM. Four kinds of SOM planes can be shown: 1. U-matrix (see SOM_UMAT) which shows clustering structure of the SOM. Either all or just part of the components can be used in calculating the U-matrix. 2. component planes: each component plane shows the values of one variable in each map unit 3. an empty plane which may be used as a base for, e.g., hit histogram visualization or labeling (see SOM_SHOW_ADD) 4. a fixed or indexed color representation for showing color coding or clustering The component planes and u-matrices may have colorbars showing the scale for the variable. The scale shows by default the values that variables have in the map struct. It may be changed to show the original data values (estimated by SOM_DENORMALIZE). In this case a small 'd' appears below the colorbar. The orientation of these colorbars may be changed, or they can be removed. By default the u-matrix - calculated using all variables - and all component planes are shown. This is achieved by giving command som_show(sMap) without any further arguments

sMap (struct) Map to be shown. If only this argument is specified, the function draws first the u-matrix calculated using all the variables followed by all the component planes.

(M is the number of map units) Optional arguments must be given as 'argID',value -pairs 'comp' Defines the variabels to be shown as component planes. (vector) 1xN or Nx1 vector with integer positive numbers ranging from 1 to the number of variables in the map codebook (dim). This vector determines the variables to be show as component planes and their order. Note that the same component plane (the same variable index) is allowed to occur several times. (string) 'all' or '' or []. This uses all variables, that is, it's the same that using value [1:dim] where dim is the number of variables in the codebook. 'compi' Same as 'comp' but uses a Gouraud shaded color plane (made using SOM_GRID function) instead of the cell-like visualization of 'comp' (made using SOM_CPLANE). Note that the color interpolation doesn't work strictly correctly on 'hexa' grid, as it uses rectangular grid (see SURF). 'umat' Show U-matrix: value defines the variables to be used for calculating a u-matrix. (vector) as in 'comps'. However, multiple occurences of the same variable (same variable index) are ignored. (string) 'all' or '' or []. This uses all variables, that is, is the same as using value [1:dim] where dim is the number of variables in the codebook. (cell) of form {v, str} where v is a valid index vector for 'umat' (see above) and str is a string that is used as a title for the u-matrix instead of the default title 'U-matrix'. This may be useful if several u-matrices are shown in the same figure. 'umati' Same as 'umat' but uses shaded color plane (see 'compi'). 'empty' Show an empty plane (patch edges only) (string) value is used as title 'color' Define fixed RGB colors for the map units (matrix) a Mx3 matrix of RGB triples as rows (vector) a Mx1 vector of any values: sets indexed coloring using the current colormap (as SURF does) (matrix) a Mx3xN matrix of RGB triples as rows. This gives N color planes. (matrix) a Mx1xN matrix of any values: sets indexed coloring using the current colormap (as SURF does). This gives N color planes. (cell) of form {rgb, str} where rgb is a Mx3 (xN) matrix of RGB triples as rows and str is a string that is used as title(s). (cell) of form {v, str} where v is a Mx1(xN) matrix of values and str is a string that is used as title(s). 'colori' Same as 'color' but uses shaded color plane (see 'compi'). 'norm' Defines whether to use normalized or denormalized values in the colorbar. If denormalized values are used, they are acquired from SOM_DENORMALIZE function using sMap.comp_norm field. (string) 'd' (default) for denormalized values and 'n' for normalized values. The corresponding letter appears below the colorbar. 'bar' Define the direction of the colorbars for component planes and U-matrices or turn them completely off. (string) 'vert' (default), 'horiz' or 'none'. 'vert' gives vertical and 'horiz' horizontal colorbars. 'none' shows no colorbars at all. 'size' Define sizes of the units. (scalar) all units have the same size (1 by default) (vector) size Mx1, each unit gets individual size scaling (as in SOM_CPLANE) 'edge' Unit edges on component plane visualizations. (string) 'on' or 'off' determines whether the unit edges on component planes ('comp') are shown or not. Default is 'off'. Note that U-matrix and color planes are _always_ drawn without edges. 'footnote' Text on the figure (string) is printed as a movable text object on the figure where it may be moved using mouse. Default value is the string in the sMap.name field. Note: value [] gives the string, but input value '' gives no footnote a all. See VIS_FOOTNOTE for more information on the text object and ways to change its font size. 'colormap' som_show ghages the colormap by default to a gray-level map (matrix) This argument is used to set some other colormap. 'subplots' the number of subplots in y- and x-directions, as in (vector) command SUBPLOT

h (struct) .plane (vector) handles to the axes objects (subplots) .colorbar (vector) handles to the colorbars. Colorbars of empty & color planes do not exist: the corresponding value in the vector is -1 .label (vector) handles to the axis labels

The property field 'Tag' of the axis objects created by this function are set to contain string 'Cplane' if the axis contains component plane ('comp'), color plane ('color') or empty plane ('empty') and string 'Uplane' if it contains a u-matrix ('umat'). The tag is set to 'CplaneI' for planes created using 'compi' and 'colori', and 'UplaneI' for 'umati'.

Note that when interpolated shading is used in coloring ('compi' and 'colori') the standard built-in bilinear Gouraud interpolation for a SURF object is used. If the lattice is hexagonal - or anything else than rectangular in general - the result is not strictly what is looked for, especially if the map is small.

% Make random data, normalize it, and give component names % Make a map data=som_data_struct(rand(1000,3),'comp_names',{'One','Two','Three'}); data=som_normalize(data,'var'); map=som_make(data); % Do the basic visualization with som_show: u-matrix and all % component planes som_show(map); % The values shown in the colorbar are denormalized codebook values % (if denormalization is possible). To view the actual values, use % the ..., 'norm', 'n' argument pair. som_show(map,'norm','n') % Something more complex: % Show 1-2. Component planes 1 and 2 (variables 'One' and 'Two') % 3. U-matrix that is calculated only using variables % 'One' and 'Two' % with title '1,2 only' % 4. U-matrix that is calculated using all variables with the % deafult title 'U-matrix' % 5. The color code (in c) with title 'Color code' % 6. Component plane 3 (variable 'Three') % and use vertical colorbars and and the values % But first: make a continuous color code (see som_colorcode) c=som_colorcode(map,'rgb1'); som_show(map,'comp',[1 2],'umat',{1:2,'1,2 only'},'umat','all', ... 'color',{c,'Color code'},'bar','vert','norm','n','comp',3)

som_show_add
| Show hits, labels and trajectories on SOM_SHOW visualization. |

som_show_clear
| Clear hit marks, labels or trajectories from current figure. |

som_umat
| Compute unified distance matrix of self-organizing map. |

som_grid
| Visualization of a SOM grid. |

som_cplane
| Visualization of component, u-matrix and color planes. |