`mzXMLplot`

Copyright Notice

This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License.

About `mzXMLplot`

mzXMLplot is a tool for visualizing mzXML data as two-dimensional "heat maps" or "virtual gels", using the RAMP library for reading mzXML data and the GD library for generating PNG files of arbitrary size. mzXMLplot runs from the command line and comes with a number of options:

-i       the input mzXML file
-o       the output PNG image file
-s       mzXML file scan range (to be plotted), e.g -s260,5320
-m       mzXML file m/z range (to be plotted), e.g -m200,1500
-t       image type or scaling function (-t1 for linear (default), -tlog for logarithmic and -tn for the n:th root). The scale can be inverted by inserting a "-" in front, e.g -t-3.
-c       colormap (0 for grayscale (default), 1 for "heat" and 2 for "jet")
-p       pixel size, e.g -p1600,1200 for a 1600×1200 pixel map (the image will be sligtly larger including axes)
-B       background to be substracted (default 0)
-S       fraction of maximum intensity for saturation of the plot (default 1.0)
-noaxes do not plot axes

mzXMLplot plots m/z on the horizontal and time (or scan number) on the vertical axis, similar to a mass spectrum rather than a chromatogram. The ticks and labels are automatically adjusted to nice, round values and not just set at a fixed fraction of the plotted ranges. Additional color schemes can easily be implemented by modifying the source code. Suggestions for improvements are always welcome. There is also a "development" version of mzXMLplot, mzXMLplot2, that also calculates and plots the difference between two aligned LC-MS datasets. For more information, please contact the author.

Gallery

	`mzXMLplot -i E_coli.mzXML -o E_coli_1.png -s 100,1600 -m 300,1300 -p 1600,1200 -B 500000 -t -log`
	`mzXMLplot -i E_coli.mzXML -o E_coli_2.png -s 100,1600 -m 300,1300 -p 1600,1200 -B 500000 -S 0.05 -c 2`
	`mzXMLplot -i E_coli.mzXML -o E_coli_3.png -s 200,1250 -m 700,725 -p 600,600 -B 50000 -S 0.05 -c 1`
click on the thumbnails to show full size image

Download the mzXMLplot source code here. (Right-click and choose "Save Link As...".)

Compiling `mzXMLplot`

Compile mzXMLplot with: gcc -o mzXMLplot mzXMLplot.c base64.c ramp.c -I. -lgd -lm -lz

Using `mzXMLplot`

Usage: mzXMLplot -i<mzXML file> -o<output PNG file> -s<first scan>,<last scan> -m<lowest m/z>,<highest m/z> [-t<image type (scale)> -c<colormap> -p<horizontal pixels>,<vertical pixels> -B<background> -S<saturation> -noaxes]

with the options described above.

Precompiled binaries

Windows (Right-click and choose "Save Link As...".)

magnus.palmblad@gmail.com

mzXMLplot