ReadMe File for Heat_Map Script
Tarjinder Singh 
ts4@williams.edu
Williams College
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Instructions for Use
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To run the Perl script, the raw RDP files must be in a folder
specifically named rawRDP that is in the same directory as the
Perl script itself.

1. Copy and paste all the RDP files (.rdpout) to the rawRDP 
   folder.
2. Open Terminal.
3. Type in Perl, then leave a space, then either a) Type in the exact directory of 
   the Perl script,or  b) Drag the Perl file into the Terminal 
   window which automatically outputs the directory
4. Press enter.
5. The heat map and the excel spreadsheet will be generated in 
   the same directory, as heat_map.ps and overview_genus.xls
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Basic Algorithm 
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The program first saves all the filenames in rawRDP into an 
array, and reads each and every file for the organisms found.
In this process, the program filters all the organisms according
to the confidence score, and stores the frequencies into a hash
table. The number of organisms in total per file post-filtering
is also calculated in this first part.

From the hash table, the ratios of the frequency of the organisms
is then calculated and all the values are formatted and stored
into an excel file.

The Perl script then interprets the frequencies according to a 
color scale and prints Postscript commands into a separate file.
The Postscript draws the heat map in the following order:
1. boxes indicating frequency, 2. the classification of organisms,
3. gradient label, 4. # seqs 

The font, colors, spacing, confidence score, sizes of the boxes
are all parameters that could be modified in the code.