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help for plotmatrix
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Plot values of a matrix as different coloured blocks

        plotmatrix , mat(matrix_name) [ split(numlist) color(colorstyle) nodiag
                           addbox(numlist) upper lower distance(varname)
                           dunit(string) maxticks(#) ]


Description

This command will display the values of a matrix using twoway area.  Each value
of the matrix will be represented by a coloured rectangular block.  A legend is
automatically created using percentiles but the user can also specify how to
split the data.

For genetic data there is an additional function to show the genomic distances
between markers.  The genomic position is entered using the distance() option.

Updating this command

To obtain the latest version click the following to uninstall the old version

ssc uninstall plotmatrix

And click here to install the new version

ssc install plotmatrix

Options

mat(matrix_name) specifies the name of the matrix to plot. Note that for
matrices e(b) and e(V) the user must create a new matrix using the matrix
command.

split(numlist) specifies the cutpoints used in the legend. Note that if the
matrix contains values outside the range of the number list then the values
will not be plotted.  The default will be a number list containing the min, max
and 10 other percentiles.

color(string) specifies the colour of the blocks used. The default colour is
bluish gray. Note that RGB and CMYK colors are not accepted and colors should
be specified by the word list in colorstyle e.g. brown.

nodiag specifies that the diagonal of the matrix is not represented in the
graph.

addbox(numlist) specifies that areas of the graph will be enclosed within a
box.  The arguments of this option are groups of 4 numbers representing the
(y,x) points of two extreme vertices of the box.

upper specifies that only the upper diagonal matrix be plotted.

lower specifies that only the lower diagonal matrix be plotted.

distance(varname) specifies the physical distances between rows/columns in the
matrix. This is mostly useful for plotting a pairwise LD matrix to include the
genomic distances between markers.

dunit(string) specifies the units of the distances specified in the distance
variable. The default is Megabases but can be any string.

maxticks(#) specifies the maximum number of ticks on both the y and x axes. The
default is 8.

Examples

Plotting the values of a variance covariance matrix


  sysuse auto <--- click this first to load data

  reg price mpg trunk weight length turn, nocons

  mat regmat = e(V)

  plotmatrix, m(regmat) c(green) ylabel(,angle(0))

Plotting the values of a correlation matrix of a given varlist

  matrix accum R = price mpg trunk weight length turn , nocons dev

  matrix R = corr(R)

  plotmatrix, m(R) s(-1(0.25)1) c(red)

Genetic Examples

Plotting the values of a point-wise LD map (see command pwld), with boxes
around two areas defined by variables 1-5 and variables 11-18.

  .pwld l1_1-l76_2, mat(grid) .plotmatrix, mat(grid) split( 0(0.1)1 ) c(gray)
nodiag addbox(1 1 5 5 11 11 18 18)

Using the same data as above there were also map positions within the variable
posn. Thus the genomic map could be displayed as a diagonal axis with the
following command

  .plotmatrix , mat(grid) split( 0(0.1)1 ) c(gray) nodiag save l distance(posn)
dunit(Mb)


Author

Adrian Mander, MRC Human Nutrition Research, Cambridge, UK.

Email adrian.mander@mrc-hnr.cam.ac.uk

See Also
Related commands:

  plotbeta (if installed), cdfplot (if installed), graphbinary (if installed), 
  palette_all (if installed).