genhstplt(1)                                                      genhstplt(1)



NAME
       genhstplt - to plot histograms and 2-D plots on screen or paper

SYNOPSIS
       genhstplt [graph options]

DESCRIPTION
       Genhstplt is a general-purpose interface to the BSHST and BSPLT his-
       togram and 2-dimensional data plotting routines.  See the documentation
       of those routines (bshst(1) and bsplt) for instructions on operating
       them.

       The data file may have 1 or more columns of data values for each indi-
       vidual.  Before the first column of data, one may place a "type" value
       for each individual.  One can then form "groups" of values by combining
       individuals of one or more types.  If there are no type values, then
       there is only one group, consisting of all individuals in the file.
       The actual type values are completely arbitrary and need not be 1, 2,
       3, etc.  Once groups are formed, they are referred to in order as 1, 2,
       etc.

       The file may have lines at the beginning which can be skipped by the
       program.  The number of columns of data values can be detected by the
       program as long as all the columns for an individual are on the same
       line in the file.  Otherwise, the number of columns (exclusive of the
       optional type value) may be put in the file, in the line just before
       the data begin, or it may be entered into the program interactively.
       Non-numeric text can be present after the last column of data.

       Sometimes it is desirable to have one graph show two or more columns in
       Y plotted versus the same column in X.  If the data does not already
       have type values, they may be rearranged so that each column becomes a
       separate type.  One column is chosen as the X column and is copied into
       column 1 of the rearranged data, and all columns are copied sequen-
       tially into column 2 of the rearranged data and given type numbers
       equal to their original column numbers.  This rearrangement can be done
       when first reading in the data, or later by using option 15.  The same
       option can be used to restore the data to the original columnar organi-
       zation.

       Symbol types are selected by numbers from 1 to 19 and can be open and
       filled square (1 & 2), open and filled diamond (3 & 4), open and filled
       triangle (5 & 6), X and + (7 & 8), open and filled circle (9 & 10),
       open and filled inverted triangle (11 & 12), U (13), S (14), circle
       with vertical line (15), thick open circle (16), circle with central
       dot (17), small dot (18), and horizontal line (19).  As of IMOD 4.6.8,
       the same symbols appear on the screen as in the Postscript plots,
       except that 16 and 17 give open and filled circles.  0 will give no
       symbol; a negative value will produce the characters corresponding to
       the point number for each data value instead of a symbol; except that
       -2 will produce completely filled areas in histograms.

       This is an interactive program that allows entries of one option after
       another for plotting data in different ways.  In many cases, you may
       find it much more convenient to use Onegenplot, which displays a
       single X/Y plot of one or more data types or columns specified with
       command line arguments, then exits when the window is closed.  Note
       also 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.

       Genhstplt takes several standard command-line options about the graph-
       ics window: -s followed by a window size in x and y, -p followed by a
       window position in x and y, -message followed by a message to be shown
       in a message box, -tooltip followed by a tooltip for the graphics win-
       dow, and -nograph to disable the graphics window.

       Entries to Genhstplt are:

       0 for plots in the graphics window, 1 for plots only on the terminal,
          or -1 for plots always in the graphics window (default -1).  If you
          enter -1, this question will not be asked again and BSPLT will not
          ask about doing terminal plots either.  Note that if you need to use
          terminal plots, you will need to specify that option each time that
          you do a plot.

       0 if there are just data values, or 1 if there are also types, or -1 to
          have columns converted into types (default 0)

       Number of columns of data values (excluding the optional types).
          Enter -1 to have the number of columns detected automatically (the
          default), 0 if the number of columns is to be read just before the
          data, or enter the number of columns.

       Number of lines to skip at start of file.  Do not count the line
          telling the number of columns, if there is one and you just entered
          0 to the last question.

       Data file name

       IF you entered -1 to have columns converted into types, and there is
       more than one column, next enter the column to be placed into the first
       column in the rearranged data.

       IF there are types, next enter:

          Number of groups.  Enter the negative of the number if there is
             only one type per group, as a shortcut.

          IF you entered a positive number, then enter for each group:

             Number of types in group, symbol number
             The type values for the types in the group

          BUT IF you entered a negative number, then enter for each group
             the type value and the symbol number

       IF there are no type values, just enter the symbol number to be used.

       Next enter the column number of the data to be examined next.

       Next specify how the data are scaled:
          To leave the data alone, enter 0,0
          To take the logarithm after adding some base amount to the data,
             enter 1 and the base amount
          If the data are already logarithms, enter -1,0

       The program now enters BSHST, which you can skip through if desired.

       You are now at an option point, which you may return to repeatedly
       while running the program.  Your choices are:

       1 to examine a new data column, first saving the current column as
          the "previous" column
       2 or 17 to enter BSPLT and plot the column just examined as a set of Y
          values versus the previous column, as a set of X values.  With 17,
          successive points in a group will be connected by lines.
       3 to plot the column just examined versus the previous column,
          first grouping points within each group on the basis of their
          X values and forming means and standard deviations within
          groups (see below)
       4 to loop back and define new groups and/or symbols
       5 to loop back to the start of the program and open a new file
       6 to plot the current Postscript file on workstation screen
       7 or 209 to plot the current Postscript file on printer
       8 or -123 to exit the program
       9 to plot the column just examined versus the previous column as
          series of Tukey box plots, one Tukey box per group.
       10 to plot values with error bars based on S.D. values in another
          column of the data file.
       11 to group points based upon their X values in the previous
         column (as in option 3) and then divide the average of the
         current column by the average of some other column
       12 to select subsets of the data based on the values in some
          other column than the ones being plotted
       13 to divide the current data column by another column
       14 to examine a new data column while retaining the existing X values,
          i.e., without copying the current column into the "previous" column
       15 to reorganization data without types to have one type per column, or
          to restore data from this reorganization
       16 to create an ordinal column, with values from 1 to the number of
          points in a group for each group
       18 to form a linear combination of two or more columns

       If you select option 3, you first choose whether to plot error bars as
       a multiple of standard deviation or standard error of the mean, or as
       confidence limits.  Enter a positive number to get bars equal to that
       number of S.D.'s, or a negative value to get bars equal to that number
       of S.E.M.'s, or a positive number greater than 30 to get confidence
       limits at that percentage level (e.g., 90 for 90% confidence limits).
       Then, for each group of types, you will be told how many data points
       there are.  Enter the number of groupings that you want to combine
       these points into, then enter the number of points to include in each
       of the groupings, or just a / to divide the points equally among the
       groupings.  If you enter individual numbers for each grouping, they
       should add up to the total number of points in that group of types.

       If you select option 9, then when the data are plotted on the printer,
       they will appear as Tukey box plots for each group.  Each such box
       shows the median and 25 and 50 percentile values of the set of Y values
       for the group; lines and ticks show the 10 and 90 percentile points,
       and symbols are plotted for any data values outside the 10 and 90 per-
       centile levels.  The box is plotted at the mean X coordinate of the
       points in the group.

       If you select option 10, you first choose whether to plot error bars as
       a multiple of standard deviation or standard error of the mean, or as
       confidence limits.  Enter a positive number to get bars equal to that
       number of S.D.'s, or a negative value to get bars equal to that number
       of S.E.M.'s, or a positive number greater than 30 to get confidence
       limits at that percentage level (e.g., 90 for 90% confidence limits).
       If you select S.D.'s, next enter the column number in the data file
       that contains the S.D.'s.  Otherwise, enter two column numbers: the one
       with the S.D.'s and one with N's.  Both of these parameters are needed
       to plot S.E.M.'s or confidence limits.

       If you select option 11, you first enter a value for error bars as in
       option 3.  Then enter the column to divide the current column by.  Then
       specify the groupings of points for each group of data.  The default
       groupings will have nearly equal SUMS for the denominators.  The pro-
       gram will compute and print out for each set of points the following
       values: mean of previous column (X), mean of current column, SD of cur-
       rent column, mean of denominator column, mean of current divided by
       mean of denominator column (Y), SD of current divided by mean of denom-
       inator (SD associated with Y), and number of points in the set.  Error
       bars based on the resulting SD values may or may not be meaningful
       depending on the nature of the data.

       If you select option 12, first enter the number of the column that will
       be used to test whether to include data.  Then enter a lower and upper
       limit to a range of values, plus either 0 to include only values in
       that range, or 1 to exclude values in that range.  Use this option
       repeatedly to enter multiple selection criteria.  Data points will have
       to meet all of the criteria to be included in the plots.  After enter-
       ing one or more selection criteria, you must select data by specifying
       columns with option 1.  To cancel all of the criteria, specify option
       12 and enter 0 for the column.

       If you select option 13, first enter the number of the column to divide
       by, then enter lower and upper limits for the quotient, or 0,0 not to
       limit the quotient.  The current data column is not replaced, so you
       can use this option repeatedly to divide the current data column by
       different other columns.

       Option 16 is useful for graphing a sequence of values when the data
       file does not contain a column suitable for the X axis.  This option
       will create numbers in the current column from 1 up to the number of
       items in each group .  You will then have to use option 1 to select a
       new column for the Y axis, and the ordinal values will be moved into
       the "previous" column to serve as the X axis.

       If you select option 18, enter a series of pairs of numbers, first a
       coefficient then a column number, all on one line.  For example,
       "0.5,1,0.25,2,0.25,4" will form a weighted average of columns 1, 2, and
       4 with wieths 0.5, 0.25, and 0.25.  Coefficients need to add to one or
       be positive.   After entering this line, enter 0 to have to current Y
       axis data be moved to the X axis as usual, or 1 to replace it and
       retain the existing X axis data.

       There are several additional options to control plotting, most of them
       used by Onegenplot; options -4 and -5 are also generally useful if
       making postscript plots:

       -2 Enter X axis label and symbol key strings to appear to right of graph.
           Follow with the X axis label or blank for none, then with the number
           of key strings (between 0 and 8), then with the key strings on
           separate lines.
       -3 Invert display contrast to be white lines on black background, or back
           to black on white.
       -4 Enter a set of colors for selected groups, which will be applied for
           symbols, lines in both screen plots and postscript plots.  First
           enter the number of colors to be entered; 0 eliminates all color
           drawing.  Then enter 4 values that number of times: a group number
           (numbered from 1), and red, green, and blue components ranging from 0
           to 255.  A color will be ignored if the graph has fewer groups than
           the color's group number.
       -5 Enter the index of a text string to apply a color to for each color
           entered with -4; the colors will be used for the text strings that
           can be added to a postscript plot.
       -6 Enter a new value for the gap in connecting lines round symbols in
           postscript plots, or 0 for no gaps.  The value is multiplied by the
           symbol size to obtain the actual gap; the default is 1.1.
       -8 Wait until graph window is closed then exit

HISTORY
       Written by David Mastronarde, has wandered from one kind of computer and
       graphics to another over the years.

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 4.9.5                        genhstplt(1)