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.