Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells GENHSTPLT(1) GENHSTPLT(1) NAME genhstplt - to plot histograms and 2-D plots on screen or paper SYNOPSIS genhstplt DESCRIPTION GENHSTPLT is a general-purpose interface to the BSHST and BSPLT histogram 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 individual. 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 (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. Symbol types are selected by number, but the numbers have different meanings for symbols in the graphics window and in the Postscript printing file. Symbols 1 to 8 will appear on the screen as: filled and open circle, filled and open square, filled and open triangle, X and +; the same pattern repeats for numbers above 8. Symbols 1 to 19 are available for Postscript output and appear as 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). 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. Entries to the program are: 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. 0 if there are just data values, or 1 if there are also types Number of columns of data values (excluding the optional types). Enter 0 if the number of columns is to be read just before the data. 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 there are types, next enter: Number of groups. Enter the negative of the number of 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 2 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. 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 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 percentile 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 program will compute and print out for each set of points the following values: mean of previous column (X), mean of current column, SD of current column, mean of denominator column, mean of current divided by mean of denominator column (Y), SD of current divided by mean of denominator (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 entering 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. HISTORY Written by David Mastronarde, has wandered from one computer to the next over the years.