Using chrom_viewer.py to view chromatograms/scans:

The Chromatogram Viewer (chrom_viewer.py) which comes with CRAWDAD was designed to help visualize individual sets of data runs. Some examples of its use are outlined below. Currently it is run using command-line options, which are outlined below.
NB: Options are preceded with a double-dash, and options have to occur before other arguments (i.e. file names or prefixes)

Application Overview

By default runs are shown in TIC form ( w/ the --tic option ) To show other slices of data:

Main Options

--bp ( base peak )
--start_mz MZ1 ( will display a single m/z XIC - this parameter defines the lower side of an m/z bin )
--start_mz MZ1 --stop_mz MZ2 ( shows either base peak or TIC spanning from MZ1 to MZ2 )

Other notable options

--outfile=file_name.png - saves to a file rather than viewing on a screen
--linewidth=N - width of data lines
--nolegend    - hide legend
--mean        - show mean value
--vert        - show an inverted plot of two runs
--sd_hilo     - show +- 1 SD
--hide_data   - do not plot the raw data runs.
--colors=red,blue,green,...   - assign the listed colors to each data series being plotted (including mean, sd)
--meanstyle=--  - output dashed lines for mean
--sd_style, --data_style -- change style of SD and data lines 
--start_rt , --stop_rt (in minutes) -- zooms the runs into the desired range. Not actually that important since 
you can zoom manually.

(See linestyle appendix for list of styles)

run chrom_viewer.py --help for a listing of more options or chrom_viewer.py --explain_colors for a listing of usable colors

chrom_viewer.py usage scenarios

Plot the base peak chromatograms of two runs:
chrom_viewer.py --bp run_a.msmat run_b.msmat
Example
Plot the mean vs mean of two separate series of runs
chrom_viewer.py --bp --mean --hide_data --colors=red,blue CLASS_A series_a*.msmat CLASS_B series_b*.msmat
Note that you should use the 'ls' command on the starred sets of data to check that you are using the correct files

Example
Plot the mean, and +- 1 SD of two separate series of runs
chrom_viewer.py --bp --mean --sd_hilo --no_sd_zeros --sd_style=-- --hide_data --colors=red,red,red,blue,blue,blue CLASS_A series_a*.msmat CLASS_B series_b*.msmat
note that you should use the 'ls' command on the starred sets of data to check that you are using the correct files
Example
show aligned vs. aligned data on opposite axes
chrom_viewer.py --bp --vert CLASS_AL aligned.*.msmat CLASS_UNAL unaligned.*.msmat

Example
Show a set of overlaid spectra from two different sample classes at a give timepoint
chrom_viewer.py --bp --vert --scan_rt=45.0 --colors=red,red,red,blue,blue,blue CLASS_A run_a_1 run_a_2 run_a_3 CLASS_B run_b_1 run_b_2 run_b_3
Note that I list a color once for each file being plotted.

Example

Viewing Scans:
chrom_viewer.py --no_sparse --scan_no=N --offset=M run1.msmat run2.msmat ....
(for scan # N, adding M intensity counts to each successive run, in order to displace the scans vertically in the plot)

Viewing Images From a remote host

Frequently you will run chrom_viewer.py on a server containing the .msmat files, but want the X windows application to appear on your desktop/laptop. In order for this to work you will need an X Windows Server application (note the Cygwin version seems to crash some). Instructions on how to install XWin32 for UW staff can be seen here.

You'll need to make sure you connect via ssh w/ X11 forwarding -- this will generally be an option under ssh programs like putty, or when using openssh (ssh on Linux or cygwin) you can use forwarding with ssh -X servername

I cannot address potential firewall issues here. On Linux or other unices it may be worth trying xhosts +

Appendix -- list of line styles

plot line styles are short strings that typically define the line type, and possibly markers, for the plot.

These are used with the --mean_style, --sd_style, and --data_style options
i.e. chrom_viewer.py --bp --data_style=-- run1.msmat plots the data lines with dashes rather than a solid line

These are borrowed from matlab and are as defined below. To combine a line style and a specific marker, one would use '-.o' for example for a dash-dot line with circle markers.

    -     : solid line
    --    : dashed line
    -.    : dash-dot line
    :     : dotted line
    .     : points
    ,     : pixels
    o     : circle symbols
    ^     : triangle up symbols
    v     : triangle down symbols
    <     : triangle left symbols
    >     : triangle right symbols
    s     : square symbols
    +     : plus symbols
    x     : cross symbols
    D     : diamond symbols
    d     : thin diamond symbols
    1     : tripod down symbols
    2     : tripod up symbols
    3     : tripod left symbols
    4     : tripod right symbols
    h     : hexagon symbols
    H     : rotated hexagon symbols
    p     : pentagon symbols
    |     : vertical line symbols
    _     : horizontal line symbols'