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Last update on 25. Nov 2018 .
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    Export Column statistics to GnuPlot

    OCCURRENCE

    ARB_NT/SAI/Etc/Export Column statistics to GnuPlot

     

    DESCRIPTION

    • Select a valid column statistic
    • Select what kind of information should be extracted
      Information         Formula
      -------------------------------------
      G+C ratio           (G+C) / N
      G+A ratio           (G+A) / N
      Rate                mutation_sum / frequency_sum
      TT ratio            (min.mutations + transversions) / transversions
      Most freq. base     F1 / N
      2nd freq. base      F2 / N
      3rd freq. base      F3 / N
      Least freq. base    F4 / N
      A ratio             A / N
      C ratio             C / N
      G ratio             G / N
      TU ratio            (T+U) / N
      Helix               boolean (helix or not helix)
      Legend:
      -------
      A/C/G/T/U = amount of A/C/G/T/U's in each column
      N         = total amount of bases in each column
      Fx        = F1 = count of most freq. base, ..., F4 of least freq. base
    • Select if you like smoothing of the values (before they are written to file) '1' means no smoothing, '2' means each value is smoothed with its neighbor, etc. If you e.g. smooth by '21', then the statistic will contain 20 columns less than the unsmoothed stat (for each 21-tupel only one value is written, i.e. 10 values are missing on the left and 10 are missing on the right side).
    • Select a filter
    • Select a filename (specify without extension, which will be appended by ARB)
    • Press 'Save' to save to a file or Press 'Save & View' to save and start gnuplot
      In the last case you have some more options:
      • Select gnuplot-internal smoothing function
      • Select if to overlay other statistics (which were saved before)


     

    NOTES

    Pressing 'Delete all overlayed files' will delete all the files, which would be overlayed, if you press 'Save & View'.

     

    EXAMPLES

    None

     

    WARNINGS

    None

     

    BUGS

    No bugs known