pgfplotstable with .tsv file where the headers have underscores: How to avoid "Missing $ inserted"?

Question

The file I want to show is a .tsv file that I cannot edit. It looks like this:

up_gene up_chr  up_strand   up_Genome_pos
APLP2   chr11   +   129991686
BACE2   chr21   +   42617990
BRDT    chr1    +   92470856
CTBS    chr1    -   85028940
DHRS1   chr14   -   24761405

But when reading this I get a Missing $ inserted error. Minimal example:

\documentclass{article}
\usepackage{pgfplotstable}
% recommended:
\usepackage{booktabs}
\usepackage{array}
\usepackage{colortbl}

\begin{document}

\pgfplotstabletypeset[
  every even row/.style={
    before row={
      \rowcolor[gray]{0.9}
    }
  },
  every head row/.style={
    before row=\toprule,
    after row=\midrule
  },
  every last row/.style={
    after row=\bottomrule
  },
  string type,
  columns={up_gene,up_chr},
]
{results.tsv}

\end{document}

Which results in the error mentioned above, and this output:

So I have two questions:

How can I avoid the error I get? Note that the same error arise even if I remove columns={up_gene,up_chr}
How can I get the underscore in the header to show? I don't want to subscript the g in up_gene.

have you tried http://tex.stackexchange.com/questions/51192/how-to-use-underscores-with-pgfplotstable — percusse, Apr 25 '16 at 11:43
Thank you for answering. Yes, I did try to do something with columns/A_d/.style, with A_d exchanged for my header name, but I was not able to get it working. — L42, Apr 25 '16 at 12:47

egreg · Accepted Answer · 2017-09-22T20:03:09.590

You can set the column names yourself:

\documentclass{article}
\usepackage{pgfplotstable}
% recommended:
\usepackage{booktabs}
\usepackage{array}
\usepackage{colortbl}

\begin{document}

\pgfplotstabletypeset[
  string type,
  columns={up_gene,up_chr},
  columns/up_gene/.style={column name=up\_gene},
  columns/up_chr/.style={column name=up\_chr},
  every even row/.style={
    before row={
      \rowcolor[gray]{0.9}
    }
  },
  every head row/.style={
    before row=\toprule,
    after row=\midrule
  },
  every last row/.style={
    after row=\bottomrule
  },
]{results.tsv}

\end{document}

It is possible to cope with underscores in a different way, but it requires changing the category code of _, which might have adverse effects if math formulas are involved; also loading fontenc with the T1 option is necessary.

Here the two typesettings are shown side by syde: right as above, left with the columns selected by their indices and the change in the category code.

\documentclass{article}
\usepackage[T1]{fontenc}

\usepackage{pgfplotstable}
% recommended:
\usepackage{booktabs}
\usepackage{array}
\usepackage{colortbl}

\begin{document}

\pgfplotstabletypeset[
  string type,
  columns={up_gene,up_chr},
  columns/up_gene/.style={column name=up\_gene},
  columns/up_chr/.style={column name=up\_chr},
  every even row/.style={
    before row={
      \rowcolor[gray]{0.9}
    }
  },
  every head row/.style={
    before row=\toprule,
    after row=\midrule
  },
  every last row/.style={
    after row=\bottomrule
  },
]{results.tsv}
%
\begingroup\catcode`_=12
\pgfplotstabletypeset[
  string type,
  columns={[index]0,[index]1},
  every even row/.style={
    before row={
      \rowcolor[gray]{0.9}
    }
  },
  every head row/.style={
    before row=\toprule,
    after row=\midrule
  },
  every last row/.style={
    after row=\bottomrule
  },
]{results.tsv}
\endgroup

\end{document}

Thank you! Do you have a clue what I could do if I didn't know beforehand what the column names were? — L42, Apr 25 '16 at 15:43
@L42 That I don't know. In my opinion there should be a function for “postprocessing” the found column name, say for applying \textbf or similar; in this case one could apply \detokenize or do a more sophisticated approach with string substitutions. — egreg, Apr 25 '16 at 15:46
Is there any way to do this automatically. Eg if I don't know exactly know the column names but I just want to replace _ by \_ in each column name? — Peutch, Sep 22 '17 at 15:42

pgfplotstable with .tsv file where the headers have underscores: How to avoid "Missing $ inserted"?

1 Answers1