[Tex/LaTex] What are some good graphing libraries/programs for embedding in LaTeX

diagramsgraphs

The de-facto plotting program for LaTeX is, AFAIA, gnuplot.

Is there such a program for drawing graphs/diagrams? I am aware of graphviz and at first glance it appears very useful, but it is missing certain basic features such as specifying multiple rank orders (arrange left to right, top to bottom… see here) or subscripts/superscripts. It apparently allows for html formatting which in theory provides for subscripts/superscripts, but it does not seem to work. dot2tex attempts to make graphviz more LaTeX friendly, but the generated graphs are not as sharp, C style comments, which are valid in graphviz files, appear to conflict with LaTeX files, even when included as a doc file, and I, personally, can't figure out how to embed the graph as a figure as opposed to a dangling graph.

Is there a way to address some of these shortcomings:

no sub/superscripts
no figures
no comments

If not, is there a way to output the file to a more LaTeX friendly format, much like gnuplot does with its latex format, such that I can use LaTeX's math mode?

EDIT here are two pictures to better describe what I mean by graphs and/or diagrams

Diagram 1

Diagram 2

Best Answer

As the commenters mentioned, TikZ can do these graphics and use the full power of LaTeX. A main advantage is that, unlike pstricks, the package works for all output drivers, most notably PS and PDF. Everything will compile with just one (or two) latex/pdflatex run(s), no extra setup required. Not to mention the plethora of features described in the excellent 700+ pages manual (with tutorial).

While we're at it, try R and its TikZ device for plotting.

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[Tex/LaTex] What graphics packages are there for creating graphics in LaTeX documents

I've compiled this list. I don't have experience with most of these, but, if you do, please add more descriptive text to your package. If it does not appear, again, please add it. If you don't have the rep to edit, post it in a comment and @ messgage myself or the last editor. Also, if you feel that a certain element should not be in the list, remove it and leave a note in your edit explaining why it was removed.

The big ones:

#1 PGF/TikZ. The standard. As Dima said, it's "powerful, flexible, easy to use, and stunning". TikZ provides a high-level user interface. PGF provides lower-level macros.
#2 PStricks. Probably the second most used package.
#3 The default packages. More used than the others, but not by reason of being more powerful. These are mostly useful for including external images (e.g. graphicx) or combined with other packages (e.g. xcolor is used by PGF/TikZ).

Other graphics packages and programmes typically included in TeX distributions include:

pgfplots a package for creating 2D and 3D plots of mathematical functions and numerical data, using the PGF graphics framework. Supports but does not need external tools and addresses a wide range of data visualizations with high quality.
Xy-pic - Best suited to graphs and diagrams, but capabilities for other formats.
ePiX - Best for mathematical figures, creates PSTricks, tikz, or eepic macros.
MetaPost - Similar to MetaFont, outputs PostScript files. Used by Knuth. Allows direct inclusion in a LaTeX file via the emp, gmp and mpgraphics package. MetaPost is now integrated in LuaTeX via the mplib library. Using LuaTeX, you can include your metapost figures directly in the TeX/LaTeX file with the luamplib package, without using any external software.
MetaFun - An extension to MetaPost.
Mfpic - A set of (La)TeX macros providing an interface to MetaPost (or METAFONT).

Independent GUI wrappers and tools which create images suitable for inclusion in LaTeX documents include:

LaTeXPiX - Windows GUI, exports PGF LaTeX code
TPX - Another Windows GUI, more flexible outputs than LaTeXPiX
Xfig - X-Window drawing tool, saves in its own .fig file, but outputs many formats (Including PS).
Asymptote - A vector graphics language. Can embed LaTeX within the image. Outputs graphics for your document, not code, although code may be compiled as part of document compilation, with shell escape enabled. It can generate both 2D and 3D figures. 3D figures can be included in a PDF file in the PRC format which allows them to be manipulated when viewed in Adobe Reader.
Inkscape - A very powerful and well-supported SVG editor. Can be used to export TikZ code.
Ipe - A powerful vector graphics editor, with several snapping modes that make it especially suitable for variety of technical illustrations. Saves in its own .ipe file format, but outputs pdf and eps for inclusion in TeX documents. Uses LaTeX to typeset text, both labels and larger paragraphs. Supports layers and views, which make it possible to "build" illustrations incrementally in a presentation.
Knitr/Sweave - Tools that allow you to include R code directly into your LaTeX file. Sweave is the older utility and is part of base utils package in R. Knitr is a package that reimplements and extend the basic ideas in Sweave. They do much more than just generate graphics; they make inclusion of R generated graphics into a LaTeX document very easy.
KtikZ,QtikZ - A PGF/Tikz real-time compiler for GNU/Linux, based on Qt and designed to integrate into KDE it has a new version for Windows, but I haven't tested it yet). It can speed up the drawing time while at the same time allowing to code directly in TikZ code. It has a template option which allows to define user commands in an easy way as well as a menu with many common (and not so common) TikZ constructs.
GeoGebra - Award-winning free interactive geometry tool. As such it is also a vector graphics editor and a graph plotting software. Supports exporting to PSTricks, TikZ and Asymptote in addition to more traditional image formats. Available for major desktop and mobile platforms.

[Tex/LaTex] a good way to draw Dynkin diagrams in LaTeX

I would not recommend abusing the feynmf package. In the past I have used the picture environment (with the eepic package) to do precisely this.

Table 6.2 in page 185 of these lecture notes (PDF file), I typeset the Dynkin diagrams using the picture environment. I'm happy to make the code available. Here's a sample for the $A_n$ Dynkin diagram:

\begin{picture}(50,7)
\multiput(5,1)(10,0){5}{\circle{2}}
\multiputlist(10,1)(10,0)%
{{\line(1,0){8}},{\line(1,0){8}},{$\cdots$},{\line(1,0){8}}}
\multiputlist(5,3)(10,0){$\scriptscriptstyle 1$,%
$\scriptscriptstyle 2$,$\scriptscriptstyle 3$,%
$\scriptscriptstyle \ell{-}1$,$\scriptscriptstyle \ell$}
\end{picture}

The diagram is decorated with a labelling of the nodes, by the way.

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[Tex/LaTex] What graphics packages are there for creating graphics in LaTeX documents

[Tex/LaTex] a good way to draw Dynkin diagrams in LaTeX

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