Gives a high resolution plot of an ordination with minimum spanning tree (A.W.A. Murray).
Options
DIMENSIONS = scalars |
Two numbers specifying the dimensions to display on the y- and x-axes; default 2,1 |
|---|---|
TITLE = text |
Title for the graph |
WINDOW = scalar |
Window for the graph; default 1 |
KEYWINDOW = scalar |
Window for the key; default 2 |
SCREEN = string token |
Controls screen (clear, keep); default clea |
Parameters
COORDINATES = matrices or datamatrices |
Coordinates from ordination |
|---|---|
TREE = matrices |
Minimum spanning tree |
SIMILARITY = symmetric matrices |
Association matrix used to derive ordination |
SYMBOLS = factors or texts |
Symbols to label the coordinates |
PENCOORDINATES = scalars |
Pen to use for the coordinates |
PENTREE = scalars |
Pen to use for the minimum spanning tree |
Description
DMST plots a minimum spanning tree using coordinates saved, for example, from a PCO. The COORDINATES parameter specifies the coordinates for the units in the plot, using either a matrix or a pointer to a set of variates (that is, a “datamatrix”). The minimum spanning tree can be supplied using the TREE parameter, or it can be calculated from the original association matrix specified using the SIMILARITY parameter. If TREE supplies a matrix with no values, these will be set to the tree calculated from the SIMILARITY matrix. If the COORDINATES structure was originally declared with row labels the procedure will automatically use these to label the plots. Alternative symbols can be defined using the SYMBOLS parameter. You can also specify the pens to be used to plot the coordinates and tree, using parameters PENCOORDINATES and PENTREE respectively. The definition of these pens, outside the procedure, thus allows the colour, size, font and linestyle of links in the tree to be controlled. By default the coordinates are plotted with colour black and the tree with colour red, symbols are 0.8 of normal size, and the tree is plotted with a dotted line.
Options TITLE, WINDOW, KEYWINDOW and SCREEN function as usual for high resolution graphics. If the WINDOW is unset a default layout with appropriately labelled axes is produced in window 1. Axes will be scaled automatically unless limits have already been set outside the procedure.
Options: DIMENSIONS, TITLE, WINDOW, KEYWINDOW, SCREEN.
Parameters: COORDINATES, TREE, SIMILARITY, SYMBOLS, PENCOORDINATES, PENTREE.
Method
A two dimensional representation of the results of a multivariate analysis, such as a PCO, is plotted on the current high resolution graphics device. A minimum spanning tree is calculated (by HDISPLAY) from an input similarity matrix if not supplied. The tree is superimposed on the plot. The procedure uses GETATTRIBUTE to access the row labels (if any) of the input structures. The input structures are converted to variates if necessary and DGRAPH is used to plot the desired data.
Action with RESTRICT
Restrict is irrelevant with matrix input structures. It should work as expected with variates.
See also
Directives: HDISPLAY, PCO, PCP.
Commands for: Multivariate and cluster analysis, Graphics.
Example
CAPTION 'DMST example',\
!t('Data from Table 1.5 of Digby & Kempton (1987), Multivariate',\
'Analysis of Ecological Communities, Chapman & Hall, London.');\
STYLE=meta,plain
TEXT Spp,title, Spp; VALUES=!t(Agr,Alo,Anx,Arr,Dac,Fes,Hel,Hol,Ppr,Ptr,\
Lol,Lat,Tri,Anr,Her,Leo,Pla,Pot,Ran,Tar),\
'Association of species on Park Grass (Czekanowski measure)'
SYMMETRICMATRIX [ROWS=Spp] PGsim
READ [PRINT=errors] PGsim
100
75 100
88 83 100
72 95 81 100
63 87 73 93 100
85 84 93 85 77 100
57 68 65 65 67 69 100
84 89 91 88 80 87 62 100
76 88 81 90 81 85 65 91 100
63 84 73 85 88 77 62 80 81 100
33 38 33 39 44 36 50 29 22 44 100
58 79 69 85 83 73 60 76 77 83 40 100
61 64 65 70 71 69 71 62 61 71 58 80 100
29 60 46 62 58 49 40 50 57 63 20 56 40 100
46 73 59 79 82 63 50 67 67 82 46 81 67 69 100
43 32 37 38 42 40 48 37 38 36 40 45 64 0 22 100
73 68 73 69 67 77 81 69 69 62 52 70 81 30 51 57 100
29 23 25 24 27 27 36 25 29 20 17 21 36 0 8 62 40 100
67 73 70 75 73 71 72 67 67 68 54 71 78 38 53 52 87 42 100
77 92 85 93 89 89 71 91 93 89 37 85 71 59 76 41 78 28 76 100 :
LRV [ROWS=Spp; COLUMNS=3] L3
PCO [PRINT=roots] PGsim; LRV=L3
FRAME 3; SCALING=xyequal
YAXIS 3; TITLE='PCO axis 2'
XAXIS 3; TITLE='PCO axis 1'
DMST [WINDOW=3; KEY=0; TITLE=title] L3['Vectors']; SIM=PGsim