Preplot reformats the output of the analysis programs so that they may be plotted by Gnuplot. The output files could be imported into any programs. The default behavior of Preplot is what we term the ``automagic'' mode. Preplot reads the Zmapqtl output file, determines what analyses have been done, and then reformats all of these analyses in a logical way. There will be a separate graph for each trait and each chromosome. Preplot will attempt to put the results from different models in Zmapqtl and from LRmapqtl on the graphs, along with any information from the Rqtl, Eqtl and MImapqtl output file (if they exist), and a significance threshold (which can be set in the interactive menu or on the command line).
Table 4.3 shows the command line options specific to
Preplot. In general, it will not be necessary to change any options to
Preplot. Most of the proper values should have been set by other programs
in the QTL Cartographer suite. You might want to use the -L command to tell Preplot
to convert LR values into LOD scores. In any case,
the output of Preplot is ready for import into Gnuplot. There will be a number
of output files. One is a plot control file, that has commands that
Gnuplot understands. The other files simply contain two columns of numbers
for the 
and 
coordinates to plot. The names of the files indicate
what the numbers are for. They all start with a lower case c , which
indicates chromosome. Following the c is an integer indicating
which chromosome, then there is a t followed by an integer indicating
the trait. Then there is a period and a file extension that indicates the
results contained in the file. For the results of composite interval
mapping, the ``.z'' filename extension will be followed by an integer
from 1 to 7 indicating the model used for the analysis. For example, the
file c2t3.z6 would have the results of composite interval mapping for trait
3 on chromosome 2 in it.