avgstatplot(1) General Commands Manual avgstatplot(1)
NAME
avgstatplot - to plot the output of IMAVGSTAT
SYNOPSIS
avgstatplot [graph options]
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 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
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 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.
HISTORY
Written by David Mastronarde 1/23/90
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 avgstatplot(1)