avgstatplot(1)              General Commands Manual             avgstatplot(1)

       avgstatplot - to plot the output of IMAVGSTAT

       avgstatplot [graph options]

       Avgstatplot is an interactive program for displaying and plotting the
       output of the program Imavgstat.

       This output consists of mean, standard deviation, and standard error of
       the mean for all of the summing areas in a series of different data
       sets.  The summing areas were derived from a set of summing regions
       specified by an IMOD model; each summing region was divided into one or
       more summing areas.  In a single plot, you can include any collection
       of summing regions for any collection of data sets.  When you select a
       summing region, points for all of the areas within that region are
       plotted, connected by lines.  There are no lines connecting the differ-
       ent summing regions for a data set, but those different regions will
       all appear with the same symbol type.

       Symbol types are selected by number, but the numbers have different
       meanings for symbols in the graphics window and in a Postscript plot.
       See the man page for Genhstplt for details.

       Each of the data sets included in a plot may be rescaled independently;
       i.e. a particular linear scaling may be applied to all of the points in
       a data set, a different scaling may be applied to all points in another
       set, etc.  It is also possible to apply the same scaling, or the same
       form of scaling, to all data sets without entering values for each set
       separately.  Scaling may be specified in four ways:  1) One may
       directly specify a factor to multiply by and a factor to add.  4)  One
       may specify that the values for a set are all to be divided by the
       value for a specified area of that set.  3) One may specify that a
       given set should have its values shifted (without any multiplication)
       so that the mean of a particular collection of summing regions matches
       the corresponding mean for some other data set.  4) One may do a least-
       squares linear regression between the data points of the set being
       scaled and the corresponding data points of some other set, and use the
       coefficients of the regression to determine the scaling factors.  The
       data points used for regression are the means from the summing areas
       within a particular collection of summing regions.

       If you are displaying only one region, and it has more than 20 summing
       areas, then you have two options.  First, you are allowed to select a
       subset of the areas for display.  Second, you may average together suc-
       cessive segments of areas.  This is useful for obtaining an average
       density tracing for a periodic, repeating structure.

       Avgstatplot takes several standard command-line options about the
       graphics 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
       window, and -nograph to disable the graphics window.

       Entries to the program are now described in order as they are first
       encountered.  After looking at one graph, one may loop back to a vari-
       ety of different points in order to change different parameters.

       Name of statistics file output by IMAVGSTAT

       0 for plots in the graphics window, or 1 for plots only on the
          terminal.  Note that if you need to use terminal plots, you will
          need to specify that option each time that you do a plot.

       List of numbers of the sets to include in the graph.  Sets are
          numbered from 1.  You can enter ranges separated by commas,
          e.g. 1-3,7-9

       List of symbol types for these sets.  Ranges may be entered, but the
          total number of types specified must equal the total number of

       List of numbers of the regions to include in the plot.  Ranges are OK

       IF you enter only one region, and that region has more than 20 areas,
          then make the following two entries:

          Starting and ending areas to include in display, or / for all.

          / for no averaging of areas; or the interval over which to average
             areas (i.e. the period of the repeat, which need not be an
             integer value), the number of areas to roll (shift) the display
             (+ or - to shift to the right or left), and the number of areas
             to add to the display by replication.  Such areas will be added
             symmetrically, half to the beginning and half to the end of
             the display.  For example, if there are 10 repeats in 564
             areas, enter 56.4,0,0 the first time and examine the display.
             If you find that the structure that you wish to appear in the
             middle of the display (area 29 of 56) is located to the left,
             say in area 20, then you need to shift by 9.  If you want to
             display 1.5 repeats, then you need to add 28 areas to the
             display.  Thus, on a second time through, enter 56.4,9,28.

       Enter a small positive value for error bars whose size is the
          standard error of the mean times that that value; or a negative
          value for error bars that are that value times the standard
          deviation; or a large positive value for error bars showing
          confidence limits with that percentage of confidence; or 0 for
          no error bars.

       0 to plot the means of the summing areas, or 1 to plot the integrals,
          which are the means times the number of pixels.

       List of numbers of sets to rescale - ranges may be entered, or just
          Return for no rescaling, or enter / to select either all sets or
          the sets selected last time, as indicated by the prompt.

       IF you select rescaling, first enter 0 to specify scaling separately
          for each set, or 1 to apply the similar scaling to all sets.

       IF you select rescaling, next make the following entries for each
          set that you specified for rescaling:

          0 to specify scaling factors directly, 999 to divide values by the
            value in one area, or the number of another data set, if you
            wish to regress this set against the other set, or the negative
            of the number of another set, if you wish to shift this set to
            have the same mean as that set.

          IF you entered 0, next enter the factor to multiply by, and the
            amount to add after multiplication

          IF you entered 999, next enter the region number, and the number
            of the area within that region, to divide by.

          BUT, IF you entered a set number, next enter a list of the numbers
            of the regions to use for comparing the two data sets.

       Amount to offset each data set from the last in the X direction (as a
          fraction of distance between successive summing areas.

       After the last entry, you enter the subroutine BSPLT, whose operation
       is described in its man page (Bsplt(1)).

       When you return from BSPLT, enter one of the following: 1 to loop back
       to the entry of the number of SEM's or SD's for error
          bars 2 to loop back to entering the list of regions to plot 3 to
       loop back to entering the list of data sets and their symbols 4 to loop
       all the way back and read a new data file 5 to plot the current Post-
       script file on the workstation screen 6 to plot the current Postscript
       file on the printer 7 to type values to screen or output to file in
       tabular format 8 to exit

       If you plot the current Postscript file (gmeta.ps), that file will be
       closed and new plots will be placed in a new version of the file.
       Thus, if you plot the file on the workstation screen, be sure to rename
       it or plot it on the printer before generating any new plots, unless
       you don't want any printout of it.

       If you elect option 7 to type values in tabular format, you will get
       the scaled values just displayed in the last graph.  Enter a file name
       to have the table printed into a file, or Return to have it types on
       the screen.  If the file already exists, the table will be appended to
       the file.

       Written by  David Mastronarde  1/23/90

       Email bug reports to mast at colorado dot edu.

IMOD                                4.9.10                      avgstatplot(1)