dissertation.tex

%
%
% UCSD Doctoral Dissertation Template
% -----------------------------------
% http://ucsd-thesis.googlecode.com
%
%
% ----------------------------------------------------------------------
% WARNING:
%
%   This template has not endorsed by OGS or any other official entity.
%   The official formatting guide can be obtained from OGS.
%   It can be found on the web here:
%   http://ogs.ucsd.edu/AcademicAffairs/Documents/Dissertations_Theses_Formatting_Manual.pdf
%
%   No guaranty is made that this LaTeX class conforms to the official UCSD guidelines.
%   Make sure that you check the final document against the Formatting Manual.
%
%   That being said, this class has been routinely used for successful
%   publication of doctoral theses.
%
%   The ucsd.cls class files are only valid for doctoral dissertations.
%
%
% ----------------------------------------------------------------------
% GETTING STARTED:
%
%   Lots of information can be found on the project wiki:
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted
%
%
%   To make a pdf from this template use the command:
%     pdflatex template
%
%
%   To get started please read the comments in this template file
%   and make changes as appropriate.
%
%   If you successfully submit a thesis with this package please let us
%   know.
%
%
% ----------------------------------------------------------------------
% KNOWN ISSUES:
%
%   Currently only the 12pt size conforms to the UCSD requirements.
%   The 10pt and 11pt options make the footnote fonts too small.
%
%
% ----------------------------------------------------------------------
% HELP/CONTACT:
%
%   If you need help try the ucsd-thesis google group:
%   http://groups.google.com/group/ucsd-thesis
%
%
% ----------------------------------------------------------------------
% BUGS:
%
%   Please report all bugs at:
%   http://code.google.com/p/ucsd-thesis/issues/list
%
%
% ----------------------------------------------------------------------
% More control of the formatting of your thesis can be achieved through
% modifications of the included LaTeX class files:
%
%   * ucsd.cls    -- Class file
%   * uct10.clo   -- Configuration files for font sizes 10pt, 11pt, 12pt
%     uct11.clo
%     uct12.clo
%
% ----------------------------------------------------------------------



% Setup the documentclass
% default options: 12pt, oneside, final
%
% fonts: 10pt, 11pt, 12pt -- are valid for UCSD dissertations.
% sides: oneside, twoside -- note that two-sided theses are not accepted
%                            by OGS.
% mode: draft, final      -- draft mode switches to single spacing,
%                            removes hyperlinks, and places a black box
%                            at every overfull hbox (check these before
%                            submission).
% chapterheads            -- Include this if you want your chapters to read:
%                              Chapter 1
%                              Title of Chapter
%
%                            instead of
%                              1 Title of Chapter
\documentclass[12pt,chapterheads]{ucsd}



% Include all packages you need here.
% Some standard options are suggested below.
%
% See the project wiki for information on how to use
% these packages. Other useful packages are also listed there.
%
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted



%% AMS PACKAGES - Chances are you will want some or all
%    of these if writing a dissertation that includes equations.
%  \usepackage{amsmath, amscd, amssymb, amsthm}

%% GRAPHICX - This is the standard package for
%    including graphics for latex/pdflatex.
\usepackage{scrextend}
\usepackage{pslatex}
\usepackage{graphicx}

%% CAPTION
% This overrides some of the ugliness in ucsd.cls and
% allows the text to be double-spaced while letting figures,
% tables, and footnotes to be single-spaced--all OGS requirements.
% NOTE: Must appear after graphics and ams math
\makeatletter
\gdef\@ptsize{2}% 12pt documents
\let\@currsize\normalsize
\makeatother
\usepackage{setspace}
\doublespace
\usepackage[font=small, width=0.9\textwidth]{caption}
\DeclareCaptionLabelFormat{prev-page}{\hrulefill\\#1 #2 \emph{(next page)}}
\usepackage{subfig}

%% SUBFIG - Use this to place multiple images in a
%    single figure.  Subfig will handle placement and
%    proper captioning (e.g. Figure 1.2(a))
% \usepackage{subfig}

%% TIMES FONT - replacements for Computer Modern
%%   This package will replace the default font with a
%%   Times-Roman font with math support.
% \usepackage[T1]{fontenc}
% \usepackage{mathptmx}
%% Palatino font (Olga's preference)
% --- BEGIN Old way of calling Palatino --- %
% \usepackage{palatino}
% \usepackage{mathpazo}
% --- END Old way of calling Palatino --- %

% --- BEGIN New way of calling Palatino --- %
\usepackage{newpxtext}
\usepackage{newpxmath}
% --- END New way of calling Palatino --- %

% --- BEGIN make verbatim smaller --- %
\usepackage{etoolbox}
\makeatletter
\patchcmd{\@verbatim}
  {\verbatim@font}
  {\verbatim@font\small}
  {}{}
\makeatother
% --- END make verbatim smaller --- %

% Add the word "Figure" in the list of figures, e.g. instead of :
%     List of Figures
%     1.1   Caption of Figure 1........1
%     1.2   Caption of Figure 2........9
% it will look like this:
%     List of Figures
%     Figure 1.1    Caption of Figure 1...1
%     Figure 1.2    Caption of Figure 2...9
% \usepackage{tocloft}
% \newlength{\mylen}
% \renewcommand{\cftfigpresnum}{\figurename\enspace}
% \settowidth{\mylen}{\cftfigpresnum\cftfigaftersnum}
% \addtolength{\cftfignumwidth}{\mylen}

%% --- Begin Natbib --- %%
% Natbib doesn't work with ShareLatex, they recommend BibLatex instead, because the compilation is built-in to BibLatex but with BibTex you have to separately compile the .bbl file
% cite package, to clean up citations in the main text. Do not remove.
% \usepackage[superscript]{cite}
\usepackage[super,sort&compress]{natbib}

% Add Bibliography to the table of contents
\usepackage[nottoc]{tocbibind}
%% --- End Natbib --- %%

%% --- Begin BibLatex --- %%
% \usepackage[utf8]{inputenc}
% \usepackage[english]{babel}
% \usepackage{csquotes}
% \usepackage[
% backend=biber,
% style=authoryear,
% sorting=nyt
% ]{biblatex}
%
% \addbibresource{chapter1}
% \addbibresource{refs}
%% --- End BibLatex ---- %%

% --- BEGIN macros and packages used in chapter 2 ---- %

% Outrigger cases use "enumerate" but some definitions extend beyond a single line and this is problematic so have to use this package
\usepackage{enumitem} % load this one
\newenvironment{longdescription}
  {\begin{description}[style=unboxed]}
  {\end{description}}

% Directory trees for chapter 2
\usepackage{dirtree}
% Set the line spacing in directory trees to be 8pt
\setlength{\DTbaselineskip}{8pt}

% Multiple columns of math equations (used in chapter 2)
\usepackage{multicol}

%% My macros
\newcommand{\0}{excluded}
\newcommand{\1}{included}
\newcommand{\anchor}{\texttt{anchor}}
\newcommand{\bonvoyage}{\texttt{bonvoyage}}
\newcommand{\outrigger}{\texttt{outrigger}}
\newcommand{\poshsplice}{\texttt{poshsplice}}
\newcommand*{\maintext}{../}
\newcommand{\XX}{\hl{\#\#\#}}

% Define new colors
\usepackage{xcolor}

% Inclusion red color
\definecolor{inclusion}{HTML}{BA1319}

% Exclusion blue color
\definecolor{exclusion}{HTML}{4B69B1}

% SI units
\usepackage{siunitx}
\DeclareSIUnit\Molar{\textsc{m}}
% \DeclareSIUnit{\Molar}{M}
% \DelcareSIUnit{\uM}{\micro\Molar}

% --- END macros and packages used in chapter 2 --- %


% Allow hyphenated urls
% \PassOptionsToPackage{hyphens}{url}




% % --- Begin use with Multibib ----
% \usepackage[resetlabels]{multibib}
% \newcites{book,article,poster}{{Books},{Journal Articles},{Conference Posters}}

% % Number the Publications
% \makeatletter
% \renewcommand*{\bibliographyitemlabel}{\@biblabel{\arabic{enumiv}}}
% \makeatother
% \renewcommand*{\bibliographyitemlabel}{[\arabic{enumiv}]}
% % --- END use with Multibib ---


%%% --- BEGIN using titlesec to adjust section fonts ---- %%%
\usepackage[T1]{fontenc}
\usepackage{titlesec}
\titleformat{\paragraph}[runin]{\bfseries}{\theparagraph}{1em}{}
\titlespacing{\paragraph}{\parindent}{0em}{2em}
\titleformat{\subparagraph}[runin]{\itshape}{\subtheparagraph}{1em}{}
%\titlespacing*{\paragraph}{\parindent}{}{}
%%% --- END using titlesec to adjust section fonts ---- %%%


%% INDEX
%   Uncomment the following two lines to create an index:
% \usepackage{makeidx}
% \makeindex
%   You will need to uncomment the \printindex line near the
%   bibliography to display the index.  Use the command
% \index{keyword}
%   within the text to create an entry in the index for keyword.
%   To compile a LaTeX document with an index the 'makeindex'
%   command will need to be run.  See the wiki for more details.

%% HYPERLINKS
%   To create a PDF with hyperlinks, you need to include the hyperref package.
%   THIS HAS TO BE THE LAST PACKAGE INCLUDED!
%   Note that the options plainpages=false and pdfpagelabels exist
%   to fix indexing associated with having both (ii) and (2) as pages.
%   Also, all links must be black according to OGS.
%   See: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=hyperdupdest
%   Note: This may not work correctly with all DVI viewers (i.e. Yap breaks).
%   NOTE: hyperref will NOT work in draft mode, as noted above.
\usepackage[colorlinks=true, pdfstartview=FitV,
            linkcolor=black, citecolor=black,
            urlcolor=black, plainpages=false,
            breaklinks=true,
            pdfpagelabels]{hyperref}
\hypersetup{ pdfauthor = {Olga Borisovna Botvinnik},
             pdftitle = {Computational analysis of single-cell alternative splicing},
             pdfkeywords = {single-cell, alternative splicing, rna processing, computational biology, bioinformatics, bayesian, machine learning, dimensionality reduction, nmf, pca, ica, non-negative matrix factorization, principal component analysis, independent component analysis},
             pdfcreator = {pdfLaTeX with hyperref package},
             pdfproducer = {pdfLaTeX} }
\urlstyle{same}

% --- BEGIN cleveref for "clever" figure references --- %
% With cleverref, can say "\cref{fig:myfig}" instead of "Figure~\ref{fig:myfig}"
% Reference multiple figures at a time, e.g. Figures 1-4
% Must be after hyperref
\usepackage{cleveref}



% Make all referenced figures and numbers bold
\crefdefaultlabelformat{#2\textbf{#1}#3}

% each of the following has two versions
%   \crefname{environmentname}{singular}{plural}, to be used mid-sentence
%   \Crefname{environmentname}{singular}{plural}, to be used at the beginning of a sentence
\crefname{table}{\textbf{table}}{\textbf{tables}}
\Crefname{table}{\textbf{Table}}{\textbf{Tables}}
\crefname{figure}{\textbf{figure}}{\textbf{figures}}
\Crefname{figure}{\textbf{Figure}}{\textbf{Figures}}
\crefname{section}{\textbf{section}}{\texttbf{section}}
\Crefname{section}{\textbf{Section}}{\textbf{Sections}}




% \usepackage{bookmark}


%% CITATIONS
% Sets citation format
% and fixes up citations madness
\usepackage{microtype}  % avoids citations that hang into the margin


%% FOOTNOTE-MAGIC
% Enables footnotes in tables, re-referencing the same footnote multiple times.
\usepackage{footnote}
\makesavenoteenv{tabular}
\makesavenoteenv{table}


%% TABLE FORMATTING MADNESS
% Enable all sorts of fun table tricks
\usepackage{rotating}  % Enables the sideways environment (NCPW)
\usepackage{array}  % Enables "m" tabular environment http://ctan.org/pkg/array
\usepackage{booktabs}  % Enables \toprule  http://ctan.org/pkg/array

%%%% --- BEGIN adjust spacing and italics of \paragraph/\subparagraph --- %%%
%\newlength{\myindent} 
%\setlength{\myindent}{\parindent} 
%\makeatletter
%\renewcommand*
%    \paragraph{\@startsection{paragraph}    % counter
%    {4}                                     % level
%    {\myindent}                             % indent
%    {-3.25ex \@plus -1ex \@minus -0.2ex}    % beforeskip
%    {0.01pt}                                % afterskip
%    {\normalfont\bfseries\nobreak\size@paragraph}%
%}
%%\renewcommand*
%%    \subparagraph{\@startsection{subparagraph}  % counter
%%    {4}                                         % level
%%    {\myindent}                                 % indent
%%    {-3.25ex \@plus -1ex \@minus -0.2ex}        % beforeskip
%%    {0.01pt}                                    % afterskip
%%    {\normalfont\itseries\nobreak\normalize}%
%%}
%\makeatother
%%%%
%
%
%%%% --- BEGIN using titlesec to adjust section fonts ---- %%%
%\usepackage[T1]{fontenc}
%\usepackage{titlesec}
%\titleformat{\paragraph}[runin]
%{\bfseries\scshape}{\theparagraph}{1em}{}
%%%% --- END using titlesec to adjust section fonts ---- %%%
%


% For auto-linebreaking of hyphenated words like "high-throughput"
\usepackage{hyphenat}

% Set tolerance of hanging words outside of margins to 0
% \tolerance=0
% OKay nvm that does really weird stuff

\begin{document}

%% FRONT MATTER
%
%  All of the front matter.
%  This includes the title, degree, dedication, vita, abstract, etc..
%  Modify the file template_frontmatter.tex to change these pages.
\include{frontmatter}





%% DISSERTATION

% A common strategy here is to include files for each of the chapters. I.e.,
% Place the chapters is separate files:
%   chapter1.tex, chapter2.tex
% Then use the commands:
\include{chapter1}
\include{chapter2}
\include{chapter3}
%
% Of course, if you prefer, you can just start with
%   \chapter{My First Chapter Name}
% and start typing away.
% \chapter{Just a Test}
% This is only a test.
% \section{A section}
% Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nulla odio
% sem, bibendum ut, aliquam ac, facilisis id, tellus. Nam posuere pede
% sit amet ipsum. Etiam dolor. In sodales eros quis pede.  Quisque sed
% nulla et ligula vulputate lacinia. In venenatis, ligula id semper
% feugiat, ligula odio adipiscing libero, eget mollis nunc erat id orci.
% Nullam ante dolor, rutrum eget, vestibulum euismod, pulvinar at, nibh.
% In sapien. Quisque ut arcu. Suspendisse potenti. Cras consequat cursus
% nulla.

% \subsection{A Figure Example}
% \label{ssec:figure_example}

% This subsection shows a sample figure.

% \begin{figure}[h]
%   \centering
%   \includegraphics[width=0.5\textwidth]{sandiego}
%   \caption[Short figure caption (must be \protect{$< 4$} lines in the list of figures)]{A picture of San Diego.  Note that figures must be on their own line (no neighboring text) and captions must be single-spaced and appear \protect\textit{below} the figure.  Captions can be as long as you want, but if they are longer than 4 lines in the list of figures, you must provide a short figure caption.\index{SanDiego}}
%   \label{fig:sandiego}
% \end{figure}

% \subsection{A Table Example}

% While in Section \ref{ssec:figure_example} Figure \ref{fig:sandiego} we had a majestic figure, here we provide a crazy table example.


% %%%% TABLE 1 %%%%
% \vspace{0.25in}
% \begin{table}[!ht]
% \caption[Short figure caption (must be \protect{$< 4$} lines in the list of tables)]{A table of when I get hungry.  Note that tables must be on their own line (no neighboring text) and captions must be single-spaced and appear \protect\textit{above} the table.  Captions can be as long as you want, but if they are longer than 4 lines in the list of figures, you must provide a short figure caption.}

% \vspace{-0.25in}
% \begin{center}
% \begin{tabular}{|p{1in}|p{2in}|p{3in}|}

% \hline
% Time of day & Hunger Level & Preferred Food \\

% \hline
% 8am & high & IHOP (French Toast) \\

% \hline
% noon & medium & Croutons (Tomato Basil Soup \& Granny Smith Chicken Salad) \\

% \hline
% 5pm & high & Bombay Coast (Saag Paneer) or Hi Thai (Pad See Ew) \\

% \hline
% 8pm & medium & Yogurt World (froyo!) \\

% \hline
% \end{tabular}
% \end{center}
% \label{tab:analysis3}
% \end{table}



% %% APPENDIX
% \appendix
% \chapter{Final notes}
% What to do about things \cite{Martin_1983}.  What did he say \cite{Rilling_Insel_1999}.
%   Remove me in case of abdominal pain.



%% END MATTER

% ---- BEGIN Bibtex (not BibLaTex) ---- %
% \printindex %% Uncomment to display the index
% \nocite{}  %% Put any references that you want to include in the bib
%               but haven't cited in the braces.
\singlespacing
\bibliographystyle{unsrtnat} 
\bibliography{paperpile}

% --- BEGIN only works with multibib --- %
% \setlength{\bibleftmargin}{0.25in}  % indent each item
% \setlength{\bibindent}{-\bibleftmargin}  % unindent the first line
% \def\baselinestretch{1.0}  % force single spacing
% \setlength{\bibitemsep}{0.16in}  % add extra space between items
% --- END only works with multibib --- %

% ---- END Bibtex (not BibLaTex) ---- %

% ---- BEGIN BibLaTex (not BibTex) ---- %
%% --- Using BibLaTex instead of BibTex --- %%
% \printbibliography
% ---- END BibLaTex (not BibTex) ---- %

\end{document}