Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

AVGSTATPLOT(1)							AVGSTATPLOT(1)

NAME
	avgstatplot - to plot the output of IMAVGSTAT

SYNOPSIS
	avgstatplot

DESCRIPTION
  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 different 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 successive segments of areas.  This is useful for obtaining
  an average density tracing for a periodic, repeating structure.

  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
  variety 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
     sets.
  
  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 Postscript 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.
  
  
HISTORY
	  Written by  David Mastronarde  1/23/90