Creating plasmid diagrams in TeX

Question

I need to create a diagram of plasmid in TeX, which looks like that:

enter image description here

The images above are slightly different but show pretty much the same thing so it would be great if I could create any of them with TeX. Of course it would be easy to just insert an image but I want to challenge myself if there's nothing like that available.

Is there any package I could use to create such diagram or should I create my own package?

This look feasible for TikZ but I’m afraid there isn’t a package or library that supports this. There is a big range on what this package should be able to implement. Have you thought about the interface/input syntax? Of course, I suggest a key-value input. Especially the second image includes a lot of information. — Qrrbrbirlbel, Jun 12 '13 at 20:00
I know what I want to insert but I haven't came up with the syntax yet. Key-value seems like a right choice but the ideal solution would be if I could choose a specific start and end point on the circle, it's color and label - would that be possible? Is TikZ easily extendable? — syntagma, Jun 12 '13 at 20:26
If I had to do this, honestly I'd probably write a python script to convert whatever the data source is (googling suggests there's some standard formats as well as a package biopython for manipulating this kind of data) into tikz code (itself possibly involving various helper macros), rather than completely building an interface in latex. Here are a couple examples from texample.net that may provide helpful inspiration/techniques: 1, 2. — kgr, Jun 12 '13 at 20:43
Are there programs that create SVG diagrams for this? You could then convert SVG to PGF/TikZ with InkScape. — Martin Schröder, Jun 14 '13 at 08:22

Tom Bombadil · Accepted Answer · 2013-06-13T20:49:34.243

I agree with kgr generating the actual data should be done by a script. To have a certain readability (in case you need to manually tweak something afterwards, like e.g. highlight something with a special color) you should definitively go with a key-value interface as Qrrbrbirlbel suggested. I'd go with pgfkeys, which is already a part of TikZ. Here's a starting point with random data:

Code

\documentclass[tikz,border=2mm]{standalone}

\tikzset{
  plasmidopt/.is family,
  plasmidopt,
  radius/.initial=3,
  height/.initial=0.3,
  color/.initial=blue!50,
  start angle/.initial=0,
  stop angle/.initial=6,
  scale/.initial=1,
}

\newcommand{\plasmidkey}[1] % access a specific key by name
{   \pgfkeysvalueof{/tikz/plasmidopt/#1}}

\newcommand{\plasmid}[1]{
  \tikzset{plasmidopt,#1} % Process Keys passed to command
  \fill[\plasmidkey{color}] (\plasmidkey{start angle}:\plasmidkey{radius}) arc (\plasmidkey{start angle}:\plasmidkey{stop angle}:\plasmidkey{radius}) -- (\plasmidkey{stop angle}:\plasmidkey{radius}+\plasmidkey{height}) arc (\plasmidkey{stop angle}:\plasmidkey{start angle}:\plasmidkey{radius}+\plasmidkey{height}) -- cycle;
}

\begin{document}

\begin{tikzpicture}
    \foreach \x in {0,5,...,359.9} % random data
    {   \pgfmathsetmacro{\mycolorvalue}{random(10,90)}
        \pgfmathsetmacro{\myheight}{0.1+rand}
        \pgfmathsetmacro{\myend}{\x+4*rnd+1}
        \plasmid{radius=3,height=\myheight,color=red!\mycolorvalue!cyan,start angle=\x,stop angle=\myend}
    }
    \draw circle (3);
\end{tikzpicture}

\end{document}

Output

enter image description here

Edit 1: What do you see when you're standing on the bottom of a manhole in New York at night, looking up?

Code

\begin{tikzpicture}
    \fill[inner color=black, outer color=black!70!blue] (0,0) circle (4.5);
    \foreach \star in {1,...,256}
    {   \pgfmathsetmacro{\starradius}{rnd/50}
        \fill[inner color=yellow,outer color=yellow!20!black] ({random(0,359)}:{3*rnd}) circle (\starradius);
    }
  \foreach \x in {0,5,...,359.9} % random data
  { \pgfmathsetmacro{\mycolorvalue}{random(10,90)}
    \pgfmathsetmacro{\myheight}{-rnd}
    \pgfmathsetmacro{\myend}{\x+4*rnd+1}
    \plasmid{radius=3,height=\myheight,color=yellow!\mycolorvalue!orange,start angle=\x,stop angle=\myend}
  }
  \fill(-4.5,-4.5) rectangle (4.5,4.5) (0,0) circle (3);
\end{tikzpicture}

Output

enter image description here

That looks really impressive with such a small amount of code. I've loaded it up in writeLaTeX if anyone wants to try adding to the example: https://www.writelatex.com/227022gsflbv — John Hammersley, Jun 12 '13 at 23:02
@percusse: If I get you right, the sky is just the inside of a giant egg? — Tom Bombadil, Jun 14 '13 at 07:46

score 16 · Answer 2 · answered Jun 12 '13 at 23:22

This is just a little add-on to Tom Bombadil's very impressive answer that shows how to feed the macro data from a table (which can also be a CSV file) using PGFPlotstable.

You can provide your data like this (values taken from Addgene):

\pgfplotstableread{
Name                    Start   End Color   Height
T7_terminator       129     1   20      0.1
T7_Terminal_primer  69      87  20      0.1
lacI                    219     1858    20      0.1
T7_transl_en_RBS        322     306 90      0.2
lacO                    367     340 90      0.2
T7_promoter         385     367 90      0.2
tet                 421     684 90      0.1
pBRrevBam_primer        492     473 90      0.1
tet                     1917        2192    50      0.3
ROP                 2667        2858    30      0.3
pGEX_3_primer       2874        2852    40      0.3
pBR322_origin       3892        3273    10      0.5
KanR2               3998        4813    10      0.6
}\datatable

to produce

\documentclass[tikz,border=2mm]{standalone}
\usepackage{pgfplots}
\tikzset{
  plasmidopt/.is family,
  plasmidopt,
  radius/.initial=3,
  height/.initial=0.3,
  color/.initial=blue!50,
  start angle/.initial=0,
  stop angle/.initial=6,
  scale/.initial=1,
}

\newcommand{\plasmidkey}[1] % access a specific key by name
{   \pgfkeysvalueof{/tikz/plasmidopt/#1}}

\newcommand{\plasmid}[1]{
  \tikzset{plasmidopt,#1} % Process Keys passed to command
  \fill[\plasmidkey{color}] (\plasmidkey{start angle}:\plasmidkey{radius}) arc (\plasmidkey{start angle}:\plasmidkey{stop angle}:\plasmidkey{radius}) -- (\plasmidkey{stop angle}:\plasmidkey{radius}+\plasmidkey{height}) arc (\plasmidkey{stop angle}:\plasmidkey{start angle}:\plasmidkey{radius}+\plasmidkey{height}) -- cycle;
}

\begin{document}

\pgfplotstableread{
Name                    Start   End Color   Height
T7_terminator       129     1   20      0.1
T7_Terminal_primer  69      87  20      0.1
lacI                    219     1858    20      0.1
T7_transl_en_RBS        322     306 90      0.2
lacO                    367     340 90      0.2
T7_promoter         385     367 90      0.2
tet                 421     684 90      0.1
pBRrevBam_primer        492     473 90      0.1
tet                     1917        2192    50      0.3
ROP                 2667        2858    50      0.3
pGEX_3_primer       2874        2852    50      0.3
pBR322_origin       3892        3273    50      0.5
KanR2               3998        4813    50      0.6
}\datatable

\def\mymaxvalue{5372}

\begin{tikzpicture}
    \pgfplotstablegetrowsof{\datatable}
    \pgfmathtruncatemacro\rows{\pgfplotsretval-1}

    \foreach \row in {0,...,\rows}{
            \pgfplotstablegetelem{\row}{Start}\of\datatable
            \pgfmathsetmacro\mystart{-\pgfplotsretval/\mymaxvalue*360+90}
            \pgfplotstablegetelem{\row}{End}\of\datatable
            \pgfmathsetmacro\myend{-\pgfplotsretval/\mymaxvalue*360+90}
            \pgfplotstablegetelem{\row}{Height}\of\datatable
            \edef\myheight{\pgfplotsretval}
            \pgfplotstablegetelem{\row}{Color}\of\datatable
            \edef\mycolorvalue{\pgfplotsretval}
            \plasmid{radius=3,height=\myheight,color=red!\mycolorvalue!cyan,start angle=\mystart,stop angle=\myend}
    }
    \draw circle (3);
\end{tikzpicture}

\end{document}

Creating plasmid diagrams in TeX

2 Answers2

Code

Output

Code

Output