[Tex/LaTex] pgfplotstable: read and manipulate multiple data files into one tabular

pgfplotstabletables

When trying to typeset a datatable I can't insert

\pgfplotstabletypeset

in a tabular environment.
What am I missing?

mwe:

\documentclass[a4paper]{article}                                           
\usepackage{pgfplotstable}
\pgfplotsset{compat=1.12}


\begin{document}                                                           

\begin{tabular}{c}                                                         
\pgfplotstabletypeset{                                                     
a b                                                                        
1 2                                                                        
3 4                                                                        
}                                                                          
\end{tabular}                                                              
\end{document}

which yields (pdflatex)

Incomplete \ifx; all text was ignored after line 12.
<inserted text> 
                \fi 
l.12     }

Alternatively, I'd like to know how to efficently typeset the following table (which was made with google docs and is not completely filled with data since I was planning to typeset it with latex)

whose data is contained in 28 different .txt files (one for each row-column combination) with 10 lines in each one, no heading or whatsoever, as this one containing the data of the first row and column

that should be "broken" in two columns in the final table (and the order of the data DOES matter).

I already know how to compose it manually (via some vim magic), and this particular case it is in fact feasible, but I am interested in the automation of the process, with an arbitrary number of columns (preferably using pgfplotstable).

Thanks in advance to all TeX superheroes out there 🙂

Best Answer

Here's a way that uses the pgfplotstable package, combined with booktabs, siunitx (for decimal alignment) and multirow (for multirows in a tabular).

First of all, the output:

I've assumed that each of your 28 data files has 10 rows (as described in your question) and is named

data11.txt  data12.txt  data13.txt data14.txt
data21.txt  data22.txt  data23.txt data24.txt
  ................
  ................
  ................
data71.txt  data72.txt  data73.txt data74.txt

You didn't specify a naming convention in your question.

The main algorithm is as follows:

for each column
- read the first data file (as is) into firstColumn
- read rows 5--10 from the first data file into secondColumn
- read rows 5--10 again from the first data file into secondColumn
- repeat the process for each row file (data21.txt, data31.txt, etc)

When it comes to typesetting the table, the duplicated rows need to be skipped, hence the:

skip rows between index={5}{10},
 skip rows between index={15}{20},
 skip rows between index={25}{30},
 skip rows between index={35}{40},
 skip rows between index={45}{50},
 skip rows between index={55}{60},
 skip rows between index={65}{70},

The multirow magic borrows from pgfplotstable-with-multirow

Here are two copies of the code: one assumes that you already have the data files, the other does not. The difference is that the version that creates the files uses the filecontents package, which creates some cruft in the header of the data files; this changes (very slightly) the reading of the data files.

References:

Code (version assuming you have data.*.txt)

% arara: pdflatex
% !arara: indent: {overwrite: yes}
\documentclass{article}

\usepackage{pgfplotstable}
\usepackage{booktabs}
\usepackage{siunitx}
\usepackage{multirow}

% create a master tabular, which will store the almagamated tabular
\pgfplotstablenew{70}{\masterTabular}

% loop through the columns
\pgfplotsinvokeforeach{1,2,3,4}{
 % read first file in each column separately
 % first column read everything
 \pgfplotstableread{data1#1.txt}\firstColumn
 % second column read only the second 5 entries
 \pgfplotstableread[skip first n=5]{data1#1.txt}\secondColumn
 % then duplicate them to make the columns match in size
 \pgfplotstablevertcat{\secondColumn}{\secondColumn}
 % now loop through the remaining rows in the column
 \pgfplotsforeachungrouped\myRowIndex in {2,...,7}{
  \pgfplotstableread{data\myRowIndex#1.txt}\dataB
  \pgfplotstablevertcat{\firstColumn}{\dataB}
  % second column
  \pgfplotstableread[skip first n=5]{data\myRowIndex#1.txt}\dataD
  \pgfplotstablevertcat{\dataD}{\dataD}
  \pgfplotstablevertcat{\secondColumn}{\dataD}
 }
 % first column into master tabular
 \pgfplotstablecreatecol[copy column from table={\firstColumn}{[index]0}]{par1#1}{\masterTabular}
 % second column into master tabular
 \pgfplotstablecreatecol[copy column from table={\secondColumn}{[index]0}]{par2#1}{\masterTabular}
}

\begin{document}

\pgfplotstabletypeset[
 % header row
 every head row/.style={
  output empty row, % hide column names
  before row={\toprule%
   \multicolumn{1}{c}{Zero}&
   \multicolumn{2}{c}{{One}}&
   \multicolumn{2}{c}{Two}&
   \multicolumn{2}{c}{Three}&
   \multicolumn{2}{c}{Four}\\
  },
  after row={\midrule},
 },
 % every 5th row in the body
 every nth row={5[-1]}{after row=\midrule},
 % last row
 every last row/.style={after row=\bottomrule},
 % column types
 display columns/0/.style={
  assign cell content/.code={%
   % the multirow bit
   \pgfmathparse{ifthenelse(int(\pgfplotstablerow/10)==\pgfplotstablerow/10,int(\pgfplotstablerow/10),-1)}%
   \ifcase\pgfmathresult% rows 0--5
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 1}}%
   \or% rows 6--10
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 2}}%
   \or% rows 11--15
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 3}}%
   \or% rows 16--20
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 4}}%
   \or% rows 21--25
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 5}}%
   \or% rows 26--30
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 6}}%
   \or% rows 31--35
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 7}}%
   \else% do nothing!
    \pgfkeyssetvalue{/pgfplots/table/@cell content}{}%%Do nothing
   \fi
  },
 },
 display columns/1/.style={string type,column type=S},
 display columns/2/.style={string type,column type=S},
 display columns/3/.style={string type,column type=S},
 display columns/4/.style={string type,column type=S},
 display columns/5/.style={string type,column type=S},
 display columns/6/.style={string type,column type=S},
 display columns/7/.style={string type,column type=S},
 display columns/8/.style={string type,column type=S},
 % skip these rows, which have been read by pgfplotstableread above
 skip rows between index={5}{10},
 skip rows between index={15}{20},
 skip rows between index={25}{30},
 skip rows between index={35}{40},
 skip rows between index={45}{50},
 skip rows between index={55}{60},
 skip rows between index={65}{70},
]{\masterTabular}

\end{document}

Code (version assuming you do not have data.*.txt)

Note: this version creates the 28 different files, data11.txt,..., data74.txt and uses skip first n=9 to account for the extra cruft from the filecontents output

% arara: pdflatex
% !arara: indent: {overwrite: yes}
\documentclass{article}

\usepackage{pgfplotstable}
\usepackage{booktabs}
\usepackage{siunitx}
\usepackage{multirow}
\usepackage{filecontents}

\begin{filecontents}{data11.txt}
11.1
11.2
11.3
11.4
11.5
11.6
11.7
11.8
11.9
11.10
\end{filecontents}
\begin{filecontents}{data21.txt}
21.1
21.2
21.3
21.4
21.5
21.6
21.7
21.8
21.9
21.10
\end{filecontents}
\begin{filecontents}{data31.txt}
31.1
31.2
31.3
31.4
31.5
31.6
31.7
31.8
31.9
31.10
\end{filecontents}
\begin{filecontents}{data41.txt}
41.1
41.2
41.3
41.4
41.5
41.6
41.7
41.8
41.9
41.10
\end{filecontents}
\begin{filecontents}{data51.txt}
51.1
51.2
51.3
51.4
51.5
51.6
51.7
51.8
51.9
51.10
\end{filecontents}
\begin{filecontents}{data61.txt}
61.1
61.2
61.3
61.4
61.5
61.6
61.7
61.8
61.9
61.10
\end{filecontents}
\begin{filecontents}{data71.txt}
71.1
71.2
71.3
71.4
71.5
71.6
71.7
71.8
71.9
71.10
\end{filecontents}
\begin{filecontents}{data12.txt}
12.1
12.2
12.3
12.4
12.5
12.6
12.7
12.8
12.9
12.10
\end{filecontents}
\begin{filecontents}{data22.txt}
22.1
22.2
22.3
22.4
22.5
22.6
22.7
22.8
22.9
22.10
\end{filecontents}
\begin{filecontents}{data32.txt}
32.1
32.2
32.3
32.4
32.5
32.6
32.7
32.8
32.9
32.10
\end{filecontents}
\begin{filecontents}{data42.txt}
42.1
42.2
42.3
42.4
42.5
42.6
42.7
42.8
42.9
42.10
\end{filecontents}
\begin{filecontents}{data52.txt}
52.1
52.2
52.3
52.4
52.5
52.6
52.7
52.8
52.9
52.10
\end{filecontents}
\begin{filecontents}{data62.txt}
62.1
62.2
62.3
62.4
62.5
62.6
62.7
62.8
62.9
62.10
\end{filecontents}
\begin{filecontents}{data72.txt}
72.1
72.2
72.3
72.4
72.5
72.6
72.7
72.8
72.9
72.10
\end{filecontents}
\begin{filecontents}{data13.txt}
13.1
13.2
13.3
13.4
13.5
13.6
13.7
13.8
13.9
13.10
\end{filecontents}
\begin{filecontents}{data23.txt}
23.1
23.2
23.3
23.4
23.5
23.6
23.7
23.8
23.9
23.10
\end{filecontents}
\begin{filecontents}{data33.txt}
33.1
33.2
33.3
33.4
33.5
33.6
33.7
33.8
33.9
33.10
\end{filecontents}
\begin{filecontents}{data43.txt}
43.1
43.2
43.3
43.4
43.5
43.6
43.7
43.8
43.9
43.10
\end{filecontents}
\begin{filecontents}{data53.txt}
53.1
53.2
53.3
53.4
53.5
53.6
53.7
53.8
53.9
53.10
\end{filecontents}
\begin{filecontents}{data63.txt}
63.1
63.2
63.3
63.4
63.5
63.6
63.7
63.8
63.9
63.10
\end{filecontents}
\begin{filecontents}{data73.txt}
73.1
73.2
73.3
73.4
73.5
73.6
73.7
73.8
73.9
73.10
\end{filecontents}
\begin{filecontents}{data14.txt}
14.1
14.2
14.3
14.4
14.5
14.6
14.7
14.8
14.9
14.10
\end{filecontents}
\begin{filecontents}{data24.txt}
24.1
24.2
24.3
24.4
24.5
24.6
24.7
24.8
24.9
24.10
\end{filecontents}
\begin{filecontents}{data34.txt}
34.1
34.2
34.3
34.4
34.5
34.6
34.7
34.8
34.9
34.10
\end{filecontents}
\begin{filecontents}{data44.txt}
44.1
44.2
44.3
44.4
44.5
44.6
44.7
44.8
44.9
44.10
\end{filecontents}
\begin{filecontents}{data54.txt}
54.1
54.2
54.3
54.4
54.5
54.6
54.7
54.8
54.9
54.10
\end{filecontents}
\begin{filecontents}{data64.txt}
64.1
64.2
64.3
64.4
64.5
64.6
64.7
64.8
64.9
64.10
\end{filecontents}
\begin{filecontents}{data74.txt}
74.1
74.2
74.3
74.4
74.5
74.6
74.7
74.8
74.9
74.10
\end{filecontents}

% create a master tabular, which will store the almagamated tabular
\pgfplotstablenew{70}{\masterTabular}

% loop through the columns
\pgfplotsinvokeforeach{1,2,3,4}{
 % read first file in each column separately
 % first column read everything
 \pgfplotstableread{data1#1.txt}\firstColumn
 % second column read only the second 5 entries
 \pgfplotstableread[skip first n=9]{data1#1.txt}\secondColumn
 % then duplicate them to make the columns match in size
 \pgfplotstablevertcat{\secondColumn}{\secondColumn}
 % now loop through the remaining rows in the column
 \pgfplotsforeachungrouped\myRowIndex in {2,...,7}{
  \pgfplotstableread{data\myRowIndex#1.txt}\dataB
  \pgfplotstablevertcat{\firstColumn}{\dataB}
  % second column
  \pgfplotstableread[skip first n=9]{data\myRowIndex#1.txt}\dataD
  \pgfplotstablevertcat{\dataD}{\dataD}
  \pgfplotstablevertcat{\secondColumn}{\dataD}
 }
 % first column into master tabular
 \pgfplotstablecreatecol[copy column from table={\firstColumn}{[index]0}]{par1#1}{\masterTabular}
 % second column into master tabular
 \pgfplotstablecreatecol[copy column from table={\secondColumn}{[index]0}]{par2#1}{\masterTabular}
}

\begin{document}

\pgfplotstabletypeset[
 % header row
 every head row/.style={
  output empty row, % hide column names
  before row={\toprule%
   \multicolumn{1}{c}{Zero}&
   \multicolumn{2}{c}{{One}}&
   \multicolumn{2}{c}{Two}&
   \multicolumn{2}{c}{Three}&
   \multicolumn{2}{c}{Four}\\
  },
  after row={\midrule},
 },
 % every 5th row in the body
 every nth row={5[-1]}{after row=\midrule},
 % last row
 every last row/.style={after row=\bottomrule},
 % column types
 display columns/0/.style={
  assign cell content/.code={%
   % the multirow bit
   \pgfmathparse{ifthenelse(int(\pgfplotstablerow/10)==\pgfplotstablerow/10,int(\pgfplotstablerow/10),-1)}%
   \ifcase\pgfmathresult% rows 0--5
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 1}}%
   \or% rows 6--10
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 2}}%
   \or% rows 11--15
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 3}}%
   \or% rows 16--20
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 4}}%
   \or% rows 21--25
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 5}}%
   \or% rows 26--30
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 6}}%
   \or% rows 31--35
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 7}}%
   \else% do nothing!
    \pgfkeyssetvalue{/pgfplots/table/@cell content}{}%%Do nothing
   \fi
  },
 },
 display columns/1/.style={string type,column type=S},
 display columns/2/.style={string type,column type=S},
 display columns/3/.style={string type,column type=S},
 display columns/4/.style={string type,column type=S},
 display columns/5/.style={string type,column type=S},
 display columns/6/.style={string type,column type=S},
 display columns/7/.style={string type,column type=S},
 display columns/8/.style={string type,column type=S},
 % skip these rows, which have been read by pgfplotstableread above
 skip rows between index={5}{10},
 skip rows between index={15}{20},
 skip rows between index={25}{30},
 skip rows between index={35}{40},
 skip rows between index={45}{50},
 skip rows between index={55}{60},
 skip rows between index={65}{70},
]{\masterTabular}

\end{document}

Comment

Final comment

Thanks to @percusse and his answer to text-size-in-pgfplotstable-tables you can use

\pgfplotstableset{
    my siunitx column/.style={%
        /pgfplots/table/display columns/#1/.style={%
            string type,column type=S,
        }
    }
}

which allows you to use

% columns 1 through 8 are siunitx
my siunitx column/.list={1,...,8},

here's a complete code:

% arara: pdflatex
% !arara: indent: {overwrite: yes}
\documentclass{article}

\usepackage{pgfplotstable}
\usepackage{booktabs}
\usepackage{siunitx}
\usepackage{multirow}
\usepackage{filecontents}

\begin{filecontents}{data11.txt}
11.1
11.2
11.3
11.4
11.5
11.6
11.7
11.8
11.9
11.10
\end{filecontents}
\begin{filecontents}{data21.txt}
21.1
21.2
21.3
21.4
21.5
21.6
21.7
21.8
21.9
21.10
\end{filecontents}
\begin{filecontents}{data31.txt}
31.1
31.2
31.3
31.4
31.5
31.6
31.7
31.8
31.9
31.10
\end{filecontents}
\begin{filecontents}{data41.txt}
41.1
41.2
41.3
41.4
41.5
41.6
41.7
41.8
41.9
41.10
\end{filecontents}
\begin{filecontents}{data51.txt}
51.1
51.2
51.3
51.4
51.5
51.6
51.7
51.8
51.9
51.10
\end{filecontents}
\begin{filecontents}{data61.txt}
61.1
61.2
61.3
61.4
61.5
61.6
61.7
61.8
61.9
61.10
\end{filecontents}
\begin{filecontents}{data71.txt}
71.1
71.2
71.3
71.4
71.5
71.6
71.7
71.8
71.9
71.10
\end{filecontents}
\begin{filecontents}{data12.txt}
12.1
12.2
12.3
12.4
12.5
12.6
12.7
12.8
12.9
12.10
\end{filecontents}
\begin{filecontents}{data22.txt}
22.1
22.2
22.3
22.4
22.5
22.6
22.7
22.8
22.9
22.10
\end{filecontents}
\begin{filecontents}{data32.txt}
32.1
32.2
32.3
32.4
32.5
32.6
32.7
32.8
32.9
32.10
\end{filecontents}
\begin{filecontents}{data42.txt}
42.1
42.2
42.3
42.4
42.5
42.6
42.7
42.8
42.9
42.10
\end{filecontents}
\begin{filecontents}{data52.txt}
52.1
52.2
52.3
52.4
52.5
52.6
52.7
52.8
52.9
52.10
\end{filecontents}
\begin{filecontents}{data62.txt}
62.1
62.2
62.3
62.4
62.5
62.6
62.7
62.8
62.9
62.10
\end{filecontents}
\begin{filecontents}{data72.txt}
72.1
72.2
72.3
72.4
72.5
72.6
72.7
72.8
72.9
72.10
\end{filecontents}
\begin{filecontents}{data13.txt}
13.1
13.2
13.3
13.4
13.5
13.6
13.7
13.8
13.9
13.10
\end{filecontents}
\begin{filecontents}{data23.txt}
23.1
23.2
23.3
23.4
23.5
23.6
23.7
23.8
23.9
23.10
\end{filecontents}
\begin{filecontents}{data33.txt}
33.1
33.2
33.3
33.4
33.5
33.6
33.7
33.8
33.9
33.10
\end{filecontents}
\begin{filecontents}{data43.txt}
43.1
43.2
43.3
43.4
43.5
43.6
43.7
43.8
43.9
43.10
\end{filecontents}
\begin{filecontents}{data53.txt}
53.1
53.2
53.3
53.4
53.5
53.6
53.7
53.8
53.9
53.10
\end{filecontents}
\begin{filecontents}{data63.txt}
63.1
63.2
63.3
63.4
63.5
63.6
63.7
63.8
63.9
63.10
\end{filecontents}
\begin{filecontents}{data73.txt}
73.1
73.2
73.3
73.4
73.5
73.6
73.7
73.8
73.9
73.10
\end{filecontents}
\begin{filecontents}{data14.txt}
14.1
14.2
14.3
14.4
14.5
14.6
14.7
14.8
14.9
14.10
\end{filecontents}
\begin{filecontents}{data24.txt}
24.1
24.2
24.3
24.4
24.5
24.6
24.7
24.8
24.9
24.10
\end{filecontents}
\begin{filecontents}{data34.txt}
34.1
34.2
34.3
34.4
34.5
34.6
34.7
34.8
34.9
34.10
\end{filecontents}
\begin{filecontents}{data44.txt}
44.1
44.2
44.3
44.4
44.5
44.6
44.7
44.8
44.9
44.10
\end{filecontents}
\begin{filecontents}{data54.txt}
54.1
54.2
54.3
54.4
54.5
54.6
54.7
54.8
54.9
54.10
\end{filecontents}
\begin{filecontents}{data64.txt}
64.1
64.2
64.3
64.4
64.5
64.6
64.7
64.8
64.9
64.10
\end{filecontents}
\begin{filecontents}{data74.txt}
74.1
74.2
74.3
74.4
74.5
74.6
74.7
74.8
74.9
74.10
\end{filecontents}

% create a master tabular, which will store the almagamated tabular
\pgfplotstablenew{70}{\masterTabular}

% loop through the columns
\pgfplotsinvokeforeach{1,2,3,4}{
 % read first file in each column separately
 % first column read everything
 \pgfplotstableread{data1#1.txt}\firstColumn
 % second column read only the second 5 entries
 \pgfplotstableread[skip first n=9]{data1#1.txt}\secondColumn
 % then duplicate them to make the columns match in size
 \pgfplotstablevertcat{\secondColumn}{\secondColumn}
 % now loop through the remaining rows in the column
 \pgfplotsforeachungrouped\myRowIndex in {2,...,7}{
  \pgfplotstableread{data\myRowIndex#1.txt}\dataB
  \pgfplotstablevertcat{\firstColumn}{\dataB}
  % second column
  \pgfplotstableread[skip first n=9]{data\myRowIndex#1.txt}\dataD
  \pgfplotstablevertcat{\dataD}{\dataD}
  \pgfplotstablevertcat{\secondColumn}{\dataD}
 }
 % first column into master tabular
 \pgfplotstablecreatecol[copy column from table={\firstColumn}{[index]0}]{par1#1}{\masterTabular}
 % second column into master tabular
 \pgfplotstablecreatecol[copy column from table={\secondColumn}{[index]0}]{par2#1}{\masterTabular}
}

% slightly reduce repetition of column styles
\pgfplotstableset{
    my siunitx column/.style={%
        /pgfplots/table/display columns/#1/.style={%
            string type,column type=S,
        }
    }
}

\begin{document}

\pgfplotstabletypeset[
 % header row
 every head row/.style={
  output empty row, % hide column names
  before row={\toprule%
   \multicolumn{1}{c}{Zero}&
   \multicolumn{2}{c}{{One}}&
   \multicolumn{2}{c}{Two}&
   \multicolumn{2}{c}{Three}&
   \multicolumn{2}{c}{Four}\\
  },
  after row={\midrule},
 },
 % every 5th row in the body
 every nth row={5[-1]}{after row=\cmidrule{2-9}},
 % last row
 every last row/.style={after row=\bottomrule},
 % column types
 display columns/0/.style={
  assign cell content/.code={%
   % the multirow bit
   \pgfmathparse{ifthenelse(int(\pgfplotstablerow/10)==\pgfplotstablerow/10,int(\pgfplotstablerow/10),-1)}%
   \ifcase\pgfmathresult% rows 0--5
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 1}}%
   \or% rows 6--10
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 2}}%
   \or% rows 11--15
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 3}}%
   \or% rows 16--20
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 4}}%
   \or% rows 21--25
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 5}}%
   \or% rows 26--30
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 6}}%
   \or% rows 31--35
    \pgfkeyssetvalue{/pgfplots/table/@cell content}%
    {\multirow{5}{*}{Case 7}}%
   \else% do nothing!
    \pgfkeyssetvalue{/pgfplots/table/@cell content}{}%%Do nothing
   \fi
  },
 },
 % columns 1 through 8 are siunitx
 my siunitx column/.list={1,...,8},
 % skip these rows, which have been read by pgfplotstableread above
 skip rows between index={5}{10},
 skip rows between index={15}{20},
 skip rows between index={25}{30},
 skip rows between index={35}{40},
 skip rows between index={45}{50},
 skip rows between index={55}{60},
 skip rows between index={65}{70},
]{\masterTabular}

\end{document}

Show me a solution

This is "a" solution that uses row no 0 as the header. (usually the header is row no -1). So PgfplotsTable will no longer put the entries inside \csname. Notice that you need to reset the style for row no 0 if you assign some style for some columns.

\documentclass{article}
\usepackage{booktabs}
\usepackage{pgfplotstable}
\usepgflibrary{decorations.fractals}

\begin{document}

\pgfplotstabletypeset[
    string type,col sep=&,row sep=\\,
    header=false,
    every head row/.style={output empty row},
    every row no 0/.style={before row=\toprule,after row=\midrule},
    every last row/.style={after row=\bottomrule},
]{
    \LaTeX & \textit{italic} & \textcolor{orange}{orange} & \reflectbox{reflect} & $e^{i\pi}+1=0$ & \tikz\draw[decoration=Koch snowflake]decorate{decorate{decorate{decorate{(0,0)--(1,0)}}}}; \\
    Lorem & ipsum & dolor & sit & amet & consectetur \\
    adipisicing & elit & sed & do & eiusmod & tempor \\
}

\end{document}

Combining with cell-processing (update)

There are ≥3 stages of cell-processing. Perhaps typeset cell is the latest one. (It is even too late to be a processing because there is nothing to do with the literal content then.) Anyway, these keys will probably work as usual.

\pgfplotstabletypeset[
    string type,col sep=&,row sep=\\,
    header=false,
    every head row/.style={output empty row},
    every row no 0/.style={before row=\toprule,after row=\midrule},
    every last row/.style={after row=\bottomrule},
    /pgfplots/table/typeset cell/.code={
        \ifnum\pgfplotstablerow=0
            \ifnum\pgfplotstablecol=\pgfplotstablecols
                \pgfkeyssetvalue{/pgfplots/table/@cell content}{\bfseries\color{orange}#1\\}
            \else
                \pgfkeyssetvalue{/pgfplots/table/@cell content}{\bfseries\color{orange}#1&}
            \fi
        \else
            \ifnum\pgfplotstablecol=\pgfplotstablecols
                \pgfkeyssetvalue{/pgfplots/table/@cell content}{#1\\}
            \else
                \pgfkeyssetvalue{/pgfplots/table/@cell content}{#1&}
            \fi
        \fi
    },
]{
    \LaTeX & \textit{italic} & \textcolor{red}{R}\textcolor{green}{G}\textcolor{blue}{B} & \reflectbox{reflect} & $e^{i\pi}+1=0$ & \tikz\draw[decoration=Koch snowflake]decorate{decorate{decorate{decorate{(0,0)--(1,0)}}}}; \\
    Lorem & ipsum & dolor & sit & amet & consectetur \\
    adipisicing & elit & sed & do & eiusmod & tempor \\
}

Show me the official Solution

Same output as before

\pgfplotstabletypeset[
    string type,col sep=&,row sep=\\,
    every head row/.style={before row=\toprule,after row=\midrule},
    every last row/.style={after row=\bottomrule},
    columns/LaTeX/.style         ={column name=\LaTeX},
    columns/italic/.style        ={column name=\textit{italic}},
    columns/orange/.style        ={column name=\textcolor{orange}{orange}},
    columns/reflect/.style       ={column name=\reflectbox{reflect}},
    columns/eipi+1/.style        ={column name={$e^{i\pi}+1=0$}},
    columns/Koch snowflake/.style={column name={\tikz\draw[decoration=Koch snowflake]decorate{decorate{decorate{decorate{(0,0)--(1,0)}}}};}},
]{
    LaTeX & itslic & orange & reflect & eipi+1 & Koch snowflake \\
    Lorem & ipsum & dolor & sit & amet & consectetur \\
    adipisicing & elit & sed & do & eiusmod & tempor \\
}

Show me the reason

Turns out that this is a basic TeX phenomenon which is totally reasonable but no one will ever, logically, think about it. In the following example, I tried to pack \ttfamily into the name of a control sequence.

\documentclass{minimal}
\begin{document}
    \expandafter\let\csname\ttfamily test\endcsname\relax
\end{document}

Then

\ttfamily is expanded;
a \protect is unveiled;
TeX read \protect before \endcsname and complained.

./236210 copy.tex:7: Missing \endcsname inserted.
<to be read again> 
                   \protect 
l.7   \expandafter\let\csname\ttfamily
                                      test\endcsname\relax
?

(\protect is \relax, it cannot be part of csname. Otherwise it is logically contradictive, right?)

Back to pgfplotstable. This package did plenty of magics and inevitably it put the entry inside a csname. Then BOOM: Since \test led to \texttt to \ttfamily and to \protect, TeX complained!

So the next question may be whether I can replace \newcommand by \edef? For instance

\xdef\test{{\ttfamily test}}

The answer is still NO but for different reason. In fact, due to the design of font-switches, there is internally something like

\xdef \font@name {\curr@fontshape}

But since there is another \edef outside, the following line is executed

\xdef \OT1/cmr/m/n/10 {\OT1/cmr/m/n/10 }

So Once you apply \test... BOOM.

The following paraphrase even gives another error.

\xdef\test{\textit{test}}

Conclusion: Never rely on any specific package for, especially, tables.

Best Answer

Code (version assuming you have data.*.txt)

Code (version assuming you do not have data.*.txt)

Comment

Final comment

Related Solutions

[Tex/LaTex] Use column-separator & (ampersand) inside \newenvironment

[Tex/LaTex] How to use variables (or formatting commands) in a header row of a \pgfplotstable table

Show me a solution

Combining with cell-processing (update)

Show me the official Solution

Show me the reason

Related Question