onegenplot(1)               General Commands Manual              onegenplot(1)

       onegenplot - Make an X/Y plot with genhstplt

       onegenplot  [options]  data_file

       Onegenplot is a Python script to make Genhstplt draw one X/Y plot
       then exit when its graph window is closed.  It has many default set-
       tings so that simple graphs can be viewed with a minimum of entries.

       The data file is a text file with one or more columns of data values
       for each individual item, separated by commas, spaces, or tabs.  In
       addition, the first entry for each item can be a type number or group
       identifier.  The file can have non-numeric lines at the beginning that
       need to be skipped over.  In most cases, this program can automatically
       detect both the number of columns of data values and how many lines of
       non-numeric text to skip at the beginning.  See the -ncol and -skip
       options for the limitations of this capability.

       If there are no types in the file, you can graph one or more columns of
       values versus one other column.  If there are types, you can graph one
       column versus another for one or more types.  In addition, you use a
       sequence of numbers instead of a data column for the X values, and thus
       plot the sequential values of one or more columns or types.

       Note that the graph window can be saved as a PNG file or printed from a
       popup menu brought up by right-clicking in the window.  For publica-
       tion-quality graphs in Postscript, it is necessary to run Genhstplt

       Onegenplot uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -input (-i) OR -InputDataFile       File name
              Name of file with data to plot.  If this option is not entered,
              the first non-option argument is used for the name.

       -ncol (-n) OR -NumberOfColumns      Integer
              The number of columns of data per item in the file, or 0 if the
              number is in the file on a line just before the data, or -1 if
              all the entries for a data item are on one line, so that the
              number can be determined automatically.  The default is -1.

       -skip (-sk) OR -SkipLinesAtStart    Integer
              Number of lines to skip at the beginning of the data file.  If
              this option is not entered, the program will attempt to deter-
              mine the number of lines to be ignored automatically.  This
              should work provided that any one of these conditions is the
                1) the extra lines always start with non-numeric text;
                2) the number of numeric values at the beginning of extra
              lines is fewer than the number of columns entered with -ncol
              (minus 1 if -types is entered too);
                3) extra lines start with a non-integer if -ncol is entered as
                4) extra lines start with only one number if -types is

       -columns (-col) OR -ColumnsToPlot   Multiple integers
              Numbers of the columns to plot, numbered from 1.  If more than
              one number is entered and -ordinals is not entered, the first
              number specifies the column to use for the X axis; otherwise all
              numbers specify columns to plot on the Y axis.  If there are no
              data types, multiple columns can be given for the Y axis; if
              there are data types, only one column can be listed for Y.  If
              this option is not entered, the default is 1 and 2, unless there
              is only one data column or -ordinals is entered, in which case
              the default is 1.

       -types (-ty) OR -TypesToPlot   Multiple integers
              One or more data types to plot; types are not numbered from one
              but correspond to the arbitrary type values in the data file.
              With this entry, the first column of numbers in the file will be
              read as type values, and the column after that will become the
              first column of data.  If there are type numbers in the file and
              this entry is not given, the type numbers will end up in the
              first column of data.

       -symbols (-sy) OR -SymbolsForTypes       Multiple integers
              One or more symbols to use for the different types or columns
              being plotted.  Available symbol numbers are:
                1, 2: Open and filled squares
                3, 4: Open and filled diamonds
                5, 6: Open and filled triangles
                7, 8: X and +
                9, 10: Open and filled circles
                11, 12: Open and filled inverted triangles
                13, 14: U and S
                15: Open circle with vertical line
                18: Small dot
                19: Horizontal line
                0: No symbol, points are automatically connected with lines
                -1: Draw item number at each data point
               If no, or not enough, symbol values are entered, the program
              will assign symbols in order from this list: 9, 7, 5, 8, 13, 14,
              1, 11, 3, 10, 6, 2, 12, 4, excluding any that have already been

       -connect (-con) OR -ConnectWithLines
              Draw lines between successive points within a type or column;
              this entry is not needed if the symbol is 0

       -ordinal (-o) OR -OrdinalsForXvalues
              Plot data within each column or type sequentially in X, i.e.,
              versus a set up numbers that start from 1 and increase by 1 for
              each value plotted.  This entry is implied if only one column is

       -xlog (-x) OR -XLogOrRootAndBase    Two floats
              1 to take the logarithm or 2 to take the square root of X val-
              ues, and the base to add before that operation.  A base is
              needed to avoid taking the logarithm or quare root of negative
              numbers.  An appropriate base value can also be helpful for
              spreading out the data more evenly.  The numeric axis labels on
              the graph will be in the units of the data after the operation,
              e.g., in log units, not in original units.

       -ylog (-y) OR -YLogOrRootAndBase    Two floats
              1 to take the logarithm or 2 to take the square root of Y val-
              ues, and the base to add before that operation.

       -hue (-hu) OR -HueOfGroup      Text string
              This option can be used to specify a color for each group being
              plotted.  Groups are numbered from 1 and correspond to the types
              or columns being plotted in separate curves.  Enter either 4
              integers separated by commas (the group number and the red,
              green, and blue values, ranging from 0 to 255) or the group num-
              ber and a stock color name separated by a comma.  Groups without
              a color will be drawn in black.  (Successive entries accumulate)

       -stock (-st) OR -StockColorList
              List standard colors available by name in the -hue option.
              These are a subset of standard HTML color names and values.

       -axis (-a) OR -XaxisLabel      Text string
              Label for the X axis

       -keys (-k) OR -KeyLabels       Text string
              Text to display as a key for one type or column, shown along
              with that type's or column's symbol, if any, on the right side
              of the window.  Text is drawn in a large box with word wrapping
              enabled, so the key can be longer than the space on the right of
              the graph.  The program will show default keys with the column
              or type number if not enough labels are entered.  (Successive
              entries accumulate)

       -message (-m) OR -MessageBoxLine    Text string
              One line of a message to be displayed in a message box (Succes-
              sive entries accumulate)

       -tooltip (-to) OR -ToolTipLine      Text string
              One line of tooltip for the graphics window (Successive entries

       -remove (-r) OR -RemoveDataFile
              Delete input file when exiting.  This option is meant to be used
              only when running in the background, as cleanup will not occur
              if the program is interrupted with Ctrl-C.

       -help (-he) OR -usage
              Print help output

              Read parameter entries from standard input

       If the data file has 2 or more columns,
          onegenplot data_file
       will plot the second column versus the first, showing scattered open

       If the data file has at least 5 columns,
          onegenplt -col 1,3,5 -con data_file
       will plot column and 3 and 5 versus column 1, with circles and X's,
       respectively, connected by lines.

       If the data file has type numbers 10, 20, 30, and 40 and at least 5
       data columns,
         onegenplt -col 2,4 -type 20,40 -sym 10,9 data_file
       will plot column 4 versus column 2 for types 20 and 40 with closed and
       open circles, respectively.

       If the data file has has 120 lines of data in 6 columns,
          onegenplt -col 3,6 -sym 0,0 -con -ord data_file
       will plot columns 3 and 6 sequentially versus 1 to 120 with lines and
       no symbols.

       David Mastronarde


       Email bug reports to mast at colorado dot edu.

IMOD                                4.10.10                      onegenplot(1)