\documentclass[12pt,a4paper]{book} \usepackage{pictex} \usepackage{graphics} \usepackage{citesort} \usepackage{verbatim} \usepackage{rotating} % ** Macros ** \def\FastPiCTeX{F\kern-.30em\lower.5ex\hbox{A}\kern-.12emS\kern-.18em\lower-0.5ex\hbox{T}\PiCTeX} \author{ Harald Martin Stau\ss, MD \\ Dept. of Integrative Physiology \\ The University of Iowa \\ 410 Field House \\ Iowa City, IA 52245 \\ USA \\ e-mail: harald-stauss@uiowa.edu } \title{Generating Charts with \FastPiCTeX} \date{\today} \begin{document} \maketitle { \setlength{\parindent}{0pt} {\bf \FastPiCTeX:} H. M. Stau\ss, 2$^{nd}$~edition, 2008 \vfill \begin{center} Dedicated to \\ the Free Software Foundation \\ and all \TeX\ users \end{center} \vfill This manual was generated using \LaTeX\ and \PiCTeX. The sources of the \FastPiCTeX\ program together with the \LaTeX\ sources of this manual are freely available. The rules of the GNU public license apply. The author would appreciate receiving picture postcards of the home town of people who like this program. } \tableofcontents \listoffigures %\listoftables \chapter{GNU general public license} \begin{center} Version 2, June 1991 \\ \vspace*{1em} Copyright \copyright \ 1989, 1991 Free Software Foundation, Inc. \\ 675 Mass Ave, Cambridge, MA 02139, USA \\ Everyone is permitted to copy and distribute verbatim copies \\ of this license document, but changing it is not allowed. \\ \end{center} \section{Preamble} The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. 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Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. \begin{center} NO WARRANTY \end{center} \item BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. \item IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. \begin{center} END OF TERMS AND CONDITIONS \end{center} \end{enumerate} \chapter{Introduction} When I was writing my doctoral thesis in the late 80$^{th}$, I spent my total savings and bought an IBM-compatible personal computer, that was based on a 8080~microprocessor. Of course, I was using \LaTeX\ as text-processing software. Inspired by my brother Bernhard, I decided to use \PiCTeX\ to generate the charts for my thesis. However, I soon recognized that the \TeX\ version that I used at this time (PC\TeX) was not suitable to generate \PiCTeX\ charts, since I very often received messages, such as: \\ \verb|! TeX capacity exceeded, sorry [main memory size = 65536 bytes]| Finally, the excellent \TeX\ implementation from Eberhard Mattes appeared and I could use Big\TeX\ to generate my theses using the MS-DOS operating system. Later, I switched to the Linux operating system that came with the te\TeX\ implementation and memory management was no longer a limitation. Today, I am using the MikTeX implementation of \TeX\ on the MS-Windows Vista operating system. The old original files of my doctoral thesis still run smoothly through MikTeX without modifications and that is 20 years after the thesis was written. However, the use of \PiCTeX\ for generating charts is still quite time consuming, because the \PiCTeX\ macro language, although very powerful, is somewhat awkward. Pictures must be described by the \PiCTeX\ programming language and usually a lot of debugging is necessary to obtain the desired result. This may be the largest disadvantage of \PiCTeX. Otherwise, \PiCTeX\ is very advanced and offers nearly everything necessary to generate very nice charts of scientific data material. In order to overcome the time consuming part of generating the \PiCTeX\ code, I decided to write a \PiCTeX-preprocessor that does all the nasty part in generating \PiCTeX\ code. This preprocessor takes a very simple macro file as input and generates an output file containing the \PiCTeX\ code. The output file can then be included in a document by the \verb|\input| command. As with most preprocessors there are some limitations of \FastPiCTeX. First, only numerical diagrams based on data material can be generated. Second, only a limited set of commands are implemented, offering only basic instructions. Therefore, fine tuning the \PiCTeX\ code is usually still necessary. However, a working skeleton of the \PiCTeX\ file can be generated easily by \FastPiCTeX. \chapter{Installation and Usage} To use \FastPiCTeX\ you certainly need \TeX. \TeX\ was developed by Donald E. Knuth. His \TeX book \cite{4} is the basis of all packages based on the most advanced typesetting software available for almost any computer platform. In addition to \TeX\ you also need \LaTeX\ that was developed as an extension to \TeX\ by Leslie Lamport who has written the original \LaTeX\ manual \cite{3}. In addition, you need \PiCTeX\ that is described in \cite{1}. The \PiCTeX\ manual by the author of \PiCTeX, Michael J. Wichura, is an indepth description of the \PiCTeX\ system and is certainly worth to read. The \PiCTeX\ manual used to be freely available on the Internet. Currently, it is only available for purchase. Installation of \FastPiCTeX\ is as simple as unpacking the archive, and running make. A binary executable version of \FastPiCTeX\ for the MS-DOS/Windows operating system is included. Compilation of the program for other operatign systems should be straight forward with any standard C++ compiler (I have used the MinGW Compiler). \begin{verbatim} tar -xzvf fastpictex-x.y.tar.gz cd fastpictex-x.y/src make \end{verbatim} Once you have generated the executable, you are ready to generate \PiCTeX\ code in just a few seconds. \verb.fastpictex. is a command line program that accepts two parameters: the input file name and the output file name. The input file is a \FastPiCTeX\ macro file, while the output file is the \PiCTeX\ code that can be included in a \LaTeX\ document. Thus, running \FastPiCTeX\ is as simple as typing: \begin{center} \verb.fastpictex file_in file_out. \end{center} As an example, consider the very simple input file (\verb|bargraph.fpt|) that generates a bargraph with four columns and standard-error bars: \verbatiminput{bargraph.fpt} To generate a \PiCTeX\ file that can be included in any \LaTeX\ file (the \PiCTeX\ package must be included) run the command: \begin{center} \verb|fastpictex bargraph.fpt bargraph.ltx| \end{center} A \LaTeX\ document that includes the bargraph (see Fig.~\ref{bargraph}) generated by \FastPiCTeX\ could be: \begin{verbatim} \documentclass[12pt]{book} \usepackage{pictex} \begin{document} This is a pretty nice bar graph: \\ \input bargraph.ltx \end{document} \end{verbatim} \begin{figure} \input bargraph.ltx \caption[A bargraph]{\small \label{bargraph} This bargraph was produced by \FastPiCTeX\ by only four lines of input code.} \end{figure} \chapter{The macro language} The \FastPiCTeX\ macro language consists of a few commands that can be used to design a chart. The series of comands that compose a chart are generally written to a file using a text editor, such as emacs or vi. A command always starts in the first column of a line. Following the command word at least one whitespace character must be inserted before the parameters for the command are added. The parameters for the commands are also separated by whitspace characters and can continue in subsequent lines. However, if several lines are used for one command, then the subsequent lines must start with at least one whitespace character (instead of with a command word). As an example, consider the following macro for the line graph shown in Fig.~\ref{linegraph}: \verbatiminput{linegraph.fpt} \begin{figure} \input linegraph.ltx \caption[A linegraph]{\small \label{linegraph} A linegraph.} \end{figure} In this example, the \verb.x. and \verb.y. commands are spread over two lines. Note, that the second lines for these commands start with whitespace characters. Whitespace characters can be blanks or tabulators. It is also possible to design charts with more than one series of data. For each series of data, commands must be provided as demonstrated in the next example. The example consists of three series of xy charts. The resulting chart is shown in Fig.~\ref{xygraph}. Note, that the three data series are automatically distinguished by different symbols (i.e. by filled circles, open circles, and by diamonds). \verbatiminput{xygraph.fpt} \begin{figure} \input xygraph.ltx \caption[A XY-graph with three series]{\small \label{xygraph} A XY-graph with three series.} \end{figure} In addition, it is possible to combine different graph types in one chart. Consider an example, in which the data points of an XY-Graph should be connected by lines. A macro file for such a chart composition is shown in the next example (Fig.~\ref{mixgraph}). \begin{verbatim} type xy x 1 2 3 4 5 y 9 12 15 17 19 dx 0.5 0.6 0.4 0.5 0.7 dy 0.8 0.9 1.2 2.0 2.4 type line x 1 2 3 4 5 y 9 12 15 17 19 \end{verbatim} \begin{figure} \input mixgraph.ltx \caption[A graph with different chart types]{\small \label{mixgraph} A graph with different chart types.} \end{figure} If a chart that consists of several series is to be composed, it is important to understand, how \FastPiCTeX\ handels the order of the commands. If a command word occurs for the first time, the command belongs to the first series. If the command word appears for a second or third time, it belongs to the second or third series. Therefore, the example that generated Fig.~\ref{mixgraph} could have also been written as: \begin{verbatim} type xy type line x 1 2 3 4 5 x 1 2 3 4 5 y 9 12 15 17 19 y 9 12 15 17 19 dx 0.5 0.6 0.4 0.5 0.7 dy 0.8 0.9 1.2 2.0 2.4 \end{verbatim} In the following sections of this chapter, the various commands are described in detail. For each command, examples are given as to how to use the commands. \section{Comments, the \% command} To add comments, use the command word \%. As an example, the macro code for one of the former examples (Fig~\ref{mixgraph}) can be written as: \verbatiminput{mixgraph.fpt} \section{The size command} The size command allows to define the width and height of the plot. The parameters of the size command are the width and the height of the chart which must both be given in units of centimeters (cm). If no size command is given, the width and height both default to 6~cm. The output of the following example is shown in figure~\ref{size}. \verbatiminput{size.fpt} \begin{figure} \input size.ltx \caption[An example with a non-standard size]{\small \label{size} An example with a non-standard size.} \end{figure} \section{The type command} The type command defines what kind of chart should be generated. The available chart types are: \begin{itemize} \item XY-graphs \item line graphs \item bar graphs \end{itemize} Please keep in mind, that you must enter a type command for every series in your chart. It is \textbf{not} possible to define the chart type once for all series! \subsection{XY-Graphs} To generate a XY-graph, simply use ``\verb|type xy|''. An example is given in Fig.~\ref{xygraph}. With XY-graphs it is sometimes interesting to study the correlation between the two variables X and Y. With \FastPiCTeX\ this can be accomplished by the ``\verb|tline|'' command explained later. \subsection{Line-Graphs} To generate a line-graph, use ``\verb|type line|''. An example is given in Fig.~\ref{linegraph}. \subsection{Bar-Graphs} To generate a bar-graph, use the command ``\verb|type bar|''. An example is given in Fig.~\ref{bargraph}. The x-coordinates of bar-graphs always start at~1 and increase by steps of~1. Therefore, the x~command for a bar graph may consist of only the letter~x and no actual x-coordinates. \section{The tline command - Regression lines} The ``\verb|tline|'' command generates regression lines and the linear regression equation for XY-graphs. The ``\verb|tline|'' command is followed by a parameter that can be 0, 1, or 2. A parameter of 0 is equivalent to not type the ``\verb|tline|'' command at all. \begin{description} \item []\verb|tline 0| no regression line and no linear regression equation. \item []\verb|tline 1| regression line but no linear regression equation. \item []\verb|tline 2| regression line and linear regression equation. \end{description} Below is the \FastPiCTeX\ code of a small example with regression lines. The corresponding graph is shown in Fig.~\ref{tline_easy}. Please note that the linear regression equation is only printed for the second XY-graph because the parameter for the \verb|tline| command for the first XY-graph is ``1''. \verbatiminput{tline_easy.fpt} \begin{figure}[htb] \input tline_easy.ltx \caption[A small example with regression lines]{\small \label{tline_easy} A small example with regression lines.} \end{figure} A more complex example of a \FastPiCTeX\ file with regression lines is shown below and the corresponding graph is povided in Fig.~\ref{tline_complex}. The \verb|\begin{sideways} ... \end{sideways}| environment used in this example requires the rotating package. \verbatiminput{tline_complex.fpt} \begin{figure} \input tline_complex.ltx \caption[A complex example with regression lines]{\small \label{tline_complex} A complex example with regression lines. The legend was moved from the right side of the figure to the bottom by editing the \LaTeX\ file of the diagram.} \end{figure} \section{The x command} The x command is used to define the x-coordinates. A x~command is required for every series in a chart. However, the actual x~coordinates may be omitted (i.e. the x~command consists of only the letter~x). In this case the x-values are assumed to start at~1 and increase by steps of~1. For example, consider the following graph that is composed of bar, line, and xy series (Fig.~\ref{x-command}): \verbatiminput{x-command.fpt} The bars and lines of the resulting graph (Fig.~\ref{x-command}) have their x-coordinates at 1, 2, 3, and 4. These x-coordinates are automatically defined by \FastPiCTeX. \begin{figure} \input x-command.ltx \caption[An example without x-coordinates]{\small \label{x-command} An example without x-coordinates.} \end{figure} \section{The xticlabels command} The xticlabels command allows to define labels for the tics at the x-axis. Examples are given in Fig.~\ref{xticlabels} that were created by the \FastPiCTeX\ commands: \verbatiminput{xticlabels1.fpt} and \verbatiminput{xticlabels2.fpt} If the labels contain blanks, you may enclose the entire label in quotes as demonstrated in on of the examples. One limitation is that it is not possible to use \LaTeX\ formatting commands such as {\verb.\bf.} or {\verb.\it.} in xticlabels. \begin{center} \begin{figure} \small \input xticlabels1.ltx \input xticlabels2.ltx \caption[Examples with labels at the tics of the x-axis]{\small \label{xticlabels} Examples with labels at the tics of the x-axis.} \end{figure} \end{center} \section{The y command} The y command is used to define the y-coordinates. This command is required for every series in a graph. It is possible to add a string (enclosed in doublequotes) directly (without any whitespace) after the numbers for the y-values. This string will be printed on top of the data point in the chart. This feature allows to add asterisks to indicate that this data point is significant or to add other kind of information to a specific data point. Examples are given in Fig.~\ref{bargraph}, \ref{asterisk}, and~\ref{legend-command}. The latter one was produced by the following \FastPiCTeX\ commands: \verbatiminput{asterisk.fpt} \begin{center} \begin{figure} \small \input asterisk.ltx \caption[An example giving extra information on data points]{\small \label{asterisk} An example giving extra information on data points.} \end{figure} \end{center} \section{The dx command} The dx command can be used to define error bars in x-direction. For example, if the standard errors are given, \FastPiCTeX\ draws horizontal error bars extending to the left and to the right by $\pm$~the standard errors. An example is given in Fig.~\ref{mixgraph}. \section{The dy command} The dy command can be used to define error bars in y-direction. For example, if the standard errors are given, \FastPiCTeX\ draws vertical error bars extending up- and downwards by $\pm$~the standard errors. Examples are given in Figs.~\ref{bargraph}, \ref{mixgraph}, and \ref{x-command}. \section{The heading command} The heading command can be used to define a heading for a chart. The heading is placed above the chart. Standard \LaTeX\ formatting commands can be used as illustrated in the example given in Fig.~\ref{heading}. \verbatiminput{heading.fpt} \begin{figure} \input heading.ltx \caption[A chart with a heading]{\small \label{heading} A chart with a heading.} \end{figure} \section{The xlabel and ylabel commands} These two commands can be used to enter a label to the x- and y-axis. Like in the heading command, regular \LaTeX\ formatting instructions can be included. If the y-axis label should be rotated by 90$^\circ$, the command ``\verb.\rotatebox{}{}.'' can be used. This command is included in the graphics package distributed with most \TeX\ and \LaTeX\ distributions. However, the ``\verb.\rotatebox{}{}.'' command uses special commands that can only be handeled by some DVI-drivers, such as the DVIPS driver. Another alternative is the rotating package that offers the \verb|\begin{sideways} ... \end{sideways}| environment that has been used to generate Fig.~\ref{tline_complex}. An example using the ``\verb.\stack{}.'' command to write the y-axis label vertically is shown in the next Figure (Fig.~\ref{axislabels}). \verbatiminput{axislabels.fpt} \begin{figure} \input axislabels.ltx \caption[A chart with a heading and labels at the axis]{\small \label{axislabels} A chart with a heading and labels at the axis.} \end{figure} \section{The xgrid and ygrid commands} If these commands are given, gridlines will be drawn in the x or y direction respectively. The commands do not need any parameters. If the xgrid or ygrid commands are not given, no gridlines will be drawn. An example is given in Fig.~\ref{grids} that was generated by the following commands: \verbatiminput{grids.fpt} \begin{figure} \input grids.ltx \caption[A chart with grid lines]{\small \label{grids} A chart with grid lines.} \end{figure} \section{The legend command} If several series of data are plotted in one single diagram, one need to know which series represents which data. To add a legend to a series simply use: ``\verb|legend description of data series|''. An example is given in Fig.~\ref{legend-command} that was generated by the following \FastPiCTeX\ file: \verbatiminput{legend.fpt} \begin{figure} \input legend.ltx \caption[An example with legends]{\small \label{legend-command} An example with legends.} \end{figure} \section{The pictex command} Text following the pictex command is simply copied into the pictex file to be interpreted by \PiCTeX. This command allows adding plain \PiCTeX\ instructions to \FastPiCTeX\ files. The syntax for this command is not very complicate: ``\verb|pictex whatever you want to pass on to pictex|''. An example is provided in Fig.~\ref{pictex-command} that was generated by the following \FastPiCTeX\ code: \verbatiminput{pictex-command.fpt} \begin{figure} \input pictex-command.ltx \caption[\PiCTeX\ commands included in \FastPiCTeX]{\small \label{pictex-command} \PiCTeX\ commands included in \FastPiCTeX.} \end{figure} % Bibliography \bibliographystyle{plain} \bibliography{fastpictex} \end{document}