This R script takes the output from the blast.pl script, a hash file containing query names and their respective chromosome numbers (queryIndex) and a hash file containing hit names and their respective chromosome numbers (hitIndex).  The script outputs  either one PDF per query or per target (depending on the user's liking).  Each PDF contains nodes for all queries and targets, but unlike the output from edges.R, which is a many-to-many diagram, this script creates either a one-to-many (all targets matched by a single query) or a many-to-one (all queries which match a single target) diagram.

*These files must all be in the same directory as the R script.

**IMPORTANT**

Before this script can be run, you must ensure that there is a sub-directory named "edges".  The script creates PDF files and places them there.  If no such directory is created the following error (or something similar) will be generated:

Error in pdf(paste(outDir, targetName, ".pdf", sep = ""), width = pageWidth,  :
    unable to start device pdf

Usage:

Output:

One PDF file per target sequence is created in the sub-directory "edges".  Each filename has the structure SEQUENCENAME.pdf.

oneQueryAllHits = TRUE

oneQueryAllHits = FALSE