In LaTeX, how can I define a string variable whose content is used instead of the variable in the compiled PDF?
Let's say I'm writing a tech doc on a software and I want to define the package name in the preamble or somewhere so that if its name changes, I don't have to replace it in a lot of places but only in one place.
add the following to you preamble:
\newcommand{\newCommandName}{text to insert}
Then you can just use \newCommandName{} in the text
For more info on \newcommand, see e.g. wikibooks
Example:
\documentclass{article}
\newcommand\x{30}
\begin{document}
\x
\end{document}
Output:
30
Use \def command:
\def \variable {Something that's better to use as a variable}
Be aware that \def overrides preexisting macros without any warnings and therefore can cause various subtle errors. To overcome this either use namespaced variables like my_var or fall back to \newcommand, \renewcommand commands instead.
For variables describing distances, you would use \newlength (and manipulate the values with \setlength, \addlength, \settoheight, \settolength and \settodepth).
Similarly you have access to \newcounter for things like section and figure numbers which should increment throughout the document. I've used this one in the past to provide code samples that were numbered separatly of other figures...
Also of note is \makebox which allows you to store a bit of laid-out document for later re-use (and for use with \settolength...).
If you want to use \newcommand, you can also include \usepackage{xspace} and define command by \newcommand{\newCommandName}{text to insert\xspace}.
This can allow you to just use \newCommandName rather than \newCommandName{}.
For more detail, http://www.math.tamu.edu/~harold.boas/courses/math696/why-macros.html
I think you probably want to use a token list for this purpose:
to set up the token list
\newtoks\packagename
to assign the name:
\packagename={New Name for the package}
to put the name into your output:
\the\packagename.
Related
I am a relatively new user of Tabulator so please forgive me if I am asking anything that, perhaps, should be obvious.
I have a Tabulator report that I am able to print and create as a PDF, but the report's formatting (as shown on the screen) is not used in either output.
For printing I have used printAsHtml and printStyled=true, but this doesn't produce a printout that matches what is on the screen. I have formatted number fields (with comma separators) and these are showing correctly, but the number columns should be right-aligned but all of the columns appear as left-aligned.
I am also using Tree View where the tree rows are coloured differently to the main table, but when I print the report with a tree open it colours the whole table with the tree colours and not just the tree.
For the PDF none of the Tabulator formatting is being used. I've looked for anything similar to the printStyled option, but I can't see anything. I've also looked at the autoTable option, but I am struggling to find what to use.
I want to format the print and PDF outputs so that they look as close to the screen representation as possible.
Is there anywhere I could look that would provide examples of how to achieve the above? The Tabulator documentation is very good, but the provided examples don't appear to explain what I am trying to do.
Perhaps there are there CSS classes that I am missing or even mis-using? I have tried including .tabulator-print-table in my CSS, but I am probably not using it correctly. I also couldn't find anything equivalent for producing PDFs. Some examples would help immensely.
Thank you in advance for any advice or assistance.
Formatting is deliberately not included in these, below i will outline why:
Downloaders
Downloaded files do not contain formatted data, only the raw data, this is because a lot of the formatters create visual elements (progress bar, star formatter etc) that cannot be replicated sensibly in downloaded files.
If you want to change the format of data in the download you will need to use an accessor, the accessorDownload option is the one you want to use in this case. The accessors transform the data as it is leaving the table.
For instance we could create an accessor that prepended "Mr " to the front of every name in a column:
var mrAccessor= function(value, data, type, params, column, row){
return "Mr " + value;
}
Assign it to a columns definition:
{title:"Name", field:"name", accessorDownload:mrAccessor}
Printing
Printing also does not include the formatters, this is because when you print a Tabulator table, the whole table is actually rebuilt as a standard HTML table, which allows the printer to work out how to layout everything across multiple pages with column headers etc. The downside of this is that it is only loosely styled like a Tabulator and so formatted contents generated inside Tabulator cells will likely break when added to a normal td element.
For this reason there is also a accessorPrint option that works in the same way as the download accessor but for printing.
If you want to use the same accessor for both occasions, you can assign the function once to the accessor option and it will be applied in both instances.
Checkout the Accessor Documentation for full details.
Sometimes it is useful to assign a 'tag', which can be a simple string, to a matplotlib artist in order to later find it easily.
If we imagine a scenario where say plt.Line2D had a property called tag which can be retrieved using plt.Line2D.get_tag() it would be very easy to find it later in a complicated plot.
The only thing I can find that looks remotely similar is the group ID: for example line.set_gid() and line.get_gid(). I haven't found any good documentation on this. The only reference is this. Is this meant for such use as described above? Is it reserved for other operations in matplotlib?
This would be very useful for grouping different artists and then performing operations on them later, for example:
for line in ax.get_lines():
if line.get_tag() == 'group A'
line.set_color('red')
# or whatever other operation
Does such a thing exist?
You can use the gid for such purposes. The only side-effect is that those names will appear in a saved svg file as the gid tag.
Alternatively you can assign any attribute to a python object.
line, = plt.plot(...)
line.myid = "group A"
just make sure not to use any existing attribute in such case.
In my workflow, I have a sample sheet that contains all the samples that are supposed to be analysed + the path where to find input files + the reference genome that is supposed to be used. All of this is sample-specific.
In my config file, I have a list of reference genomes and for each of them a list of paths of files depending on the tool.
In the rule that performs the alignment of each sample, I need to load some of those files but in a sample-specific way because the reference genome might not be the same for all samples.
Here is how I tried to solve this:
params: reference=lambda wildcards: table_samples['reference'][wildcards.sample],
chrom_sizes=config[reference]['chrom_sizes']
However, when I try to run it like this, I get an error (directly when running Snakemake) saying that reference in the line of chrom_sizes=... is not defined.
Does anybody have an idea of a workaround?
EDIT: Some more information because I guess it's not really clear what I meant. Here is the relevant part of my config file.
hg19:
bwa: 'path/to/hg19/bwa/reference'
samtools: 'path/to/hg19/samtools/reference'
chrom_sizes: '...'
mm9:
bwa: 'path/to/mm9/bwa/reference'
samtools: 'path/to/mm9/samtools/reference'
chrom_sizes: '...'
And here is an example of the sample sheet.
name path reference
sample1 path/to/sample1 mm9
So, in the line reference=lambda wildcards: table_samples['reference'][wildcards.sample] I load the respective reference to be used for the current sample. Then, in chrom_sizes=config[reference]['chrom_sizes'] I need to use reference as a variable to get chrom_sizes for the correct reference genome.
I hope this makes it a bit more clear.
This is probably a ugly solution but should work.
params:
reference = table_samples['reference']['{sample}']
chrom_sizes = config[table_samples['reference']['{sample}']]['chrom_sizes']
You were defining a variable under params and attempted to pass its value within params itself; I'm not sure Snakemake can do that.
You forgot to put quotes around the reference key. Like you write it, Python interprets it as a variable.
chrom_sizes=config['reference']['chrom_sizes']
Alright, taking the information from your comments I was able to make it work. I just had to modify them a little.
As I added to my original post, I actually needed reference to be a variable in order to pull the information for every sample individually.
As #JeeYem suggested, I tried to do the following:
chrom_sizes = config[table_samples['reference']['{sample}']]['chrom_sizes']
However, it seems not to be possible to use {sample} in this context. Instead, I changed it like this:
chrom_sizes = lambda wildcards: config[table_samples['reference'][wildcards.sample]]['chrom_sizes']
For now, it works! Thanks for everyone for the contribution!
I use \newtheorem and the numbering is done automatically. Sometimes in the text I'll refer to a theorem by this number. I'd like to have a variable equal to this number, so if the theorem number changes, the references will change also.
Yes, it works through the usual \label/\ref-mechanism:
\begin{theorem}\label{thm:foo} ...
That was Theorem~\ref{thm:foo}
(You'll need two runs of LaTeX for the number to settle, you'll get a message about changed references.) Label commands "tack onto" certain things like section headers, captions, items of enumerations and, indeed, theorems and friends.
There are also extensions that can automatically distinguish sections from subsections or figures, for that, see hyperref's \autoref or the cleveref package, but don't worry about it at this point.
You need to put a \label between the \begin{yourtheorem} \end{yourtheorem} and use \ref to refer to it as usual.
You can check this link for explanations with some broader context about theorems
I'm using Doxygen to generate documentation for my code. I need to make a PDF version of this and using Doxygen's LaTeX output appears to be the way to do it.
However I've run into a number of annoying problems, and not knowing anything about LaTeX previously haven't really got much of an idea on how to approach them, and the countless references for LaTeX related things are not much help...
I worked out how to create a custom style thing in a sty file and how to get Doxygen to use it. After a lot of searching I found out how to set the page margins etc. through this, and I'm guessing the perhaps this is the file I want for doing the other things I want, but I cant seem to find any commands for doign what I want :(
The table of contents at the start of the document contains a lot of items Id rather it didn't as it makes the contents very long. Is there some way to limit this contents to just say the first two levels, rather than having entries for every single individual function, variable, etc.? Id quite like to keep all the bookmarks however. I did try the "COMPACT_LATEX" option but as well as removing items on the contents pages, it removed the bookmarks and the member lists at the start of each section, which I do really want to keep.
Is there a way to change the order of things, like putting the full class description at the start of the section, rather than after all the members and attributes?
Wow, that's kind of evil of Doxygen.
Okay, to get around the tocdepth counter problem, add the following line to your .sty file:
\AtBeginDocument{\setcounter{tocdepth}{2}}% or whatever level you want
You can set the PDF bookmarks depth to a separate value:
% requires you \usepackage{hyperref} first
\hypersetup{
bookmarksdepth = section, % of whatever level you want
}
Also note that if you have a list of figures/tables, the tocdepth must be at least 2 for them to show up.
I don't see any way of rearranging those items within the LaTeX files---Doxygen just barfs them out there, so we can't do much. You'll have to poke around the Doxygen documentation to see if there's any way to specify the order I guess. (Here's hoping!)
You're so close.
Googling on "latex contents level" brought me to LaTeX - customizing the depth of the table of contents for different parts of the thesis which suggests
\setcounter{tocdepth}{n}
where n starts at zero for only the highest level division. This is presumable defined in all the default styles, but is worth a try in doxygen.
You could write a Perl/Awk script to simply delete the unwanted lines from the table of contents. For the file burble.tex, Latex will generate the file burble.toc, which will contain lines such as:
\contentsline {subsection}{Class F rewrites}{38}
\contentsline {subsection}{Class M rewrites}{39}
\contentsline {section}{\numberline {7}Definition and properties of the translation}{44}
\contentsline {paragraph}{Well-formedness}{54}
Simple regexes will identify which levels each line belongs to, and you can filter the file based on that. Once you have the table of contents the way you want it, insert \nofiles in the appropriate place (the style sheet?), which means that Latex will read the auxiliary files but not overwrite them.