GRAPHHITS.R

Description

This R script takes the output from the blast.pl script, a hash file containing query names and their respective chromosome numbers (queryIndex), a hash file containing hit names and their respective chromosome numbers (hitIndex), and a hash file containing the coordinates of the intron/exon boundaries (IntEx).  The script outputs one PDF file per target sequence.  Each PDF file contains a diagram which shows all hits from the list of query sequences that have matches against the target with a significance level at or below the e-value passed to blast.pl.

Arguments

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

Notes

**IMPORTANT**
Before this script can be run, you must ensure that there is a sub-directory named "pdfs".  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:
The R scripts are all made so that they can be sourced into R.  From an R prompt type:

> source("graphHits.R")

Output:
One PDF file per target sequence is created in the sub-directory "pdfs".  Each filename has the structure TARGETNAME.pdf.


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