spectacle

Description:  Create an image file of an annotated spectrum.

Usage:  spectacle [options]  <annotated spec>

Input: <annotated spectrum> - a file containing one or more spectra in the following format.
    > <identifier> <m/z> [<comment>]
    <m/z> <intensity> [<label>] [<color>] *

The first line for each spectrum begins with a > followed by a unique identifier (e.g. scan number), pre-cursor m/z, and an optional, unstructured comment. A four column list of peaks follows. The first column is m/z, the second intensity, and the third and fourth optional columns contain the text annotation to appear beside the peak and the color of the peak. Here is an example annotation file.

Output:  An image file(s) of the spectrum printed to a file named '<identifier>.ext' where identifier is taken from the annotation file and ext is png, eps, or fig depending of file format. The default is eps. Options exist for controlling output file names and formats.

Options:

• -format eps|fig|png - format of output file. Default is eps.
• -html <file> - write an HTML file with all of the spectrum images. Only enabled with png format.
• -names <file> - file contains a list of identifiers and the file name to be given to each image. The given name will be followed by the appropriate extension, png, eps, or fig. Only those spectra listed in the file will have figures made.
• -title - create a title above the figure of the form <identifier> m/z=<m/z> <comment>.
• -labeltop - the labels are placed at the top of the figure instead of right above the peak.
• -nobox - no line is drawn along the top or right-hand sides of the plot.
• -script <file> - no plot is produced. Instead, all gnuplot commands are writting to the specified file. In this way, formatting not supported by spectacle can be added to the script file before being run by gnuplot.

Warning messages:

• Warning: Color <color> not recognized.

  The color given in the annotation file is not available. Supported colors are red, green, blue, and magenta. Default color is black

• Warning: HTML file cannot be created with this file format.

  The HTML file option can only be used with png file format. No HTML file will be written.