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macros.tex
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macros.tex
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%% ADDITIONAL PACKAGES %%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{xspace}
\usepackage{float} % for additional supplementary figure float
\usepackage{siunitx}
\sisetup{group-separator = {\,}}
\usepackage{mathpazo}
\usepackage{makecell}
\DeclareTextFontCommand{\emph}{\slshape}
%\DeclareTextFontCommand{\emph}{\normalfont}
% scshape small caps
\newenvironment{mydescription}[1]
{\begin{list}{}%
{\renewcommand\makelabel[1]{\slshape ##1:\hfill}%
\settowidth\labelwidth{\makelabel{#1}}%
\setlength\leftmargin{\labelwidth}
\addtolength\leftmargin{\labelsep}}}
{\end{list}}
%%%%%%%% Config the figure names and references %%%%%%%%%%%%%%
\newcommand{\figurecaption}[2]{\caption[#1]{\textbf{#1}\linebreak\hfill #2 \linebreak\hfill}}
\newcommand{\panellabel}[1]{\textbf{\color{fbbioblue}\xspace#1\xspace}}
\newcommand{\reffigure}[2]{\xspace[\ensuremath{\rhd}~\autoref{#1}{\color{fbbioblue} #2}]\xspace}
\newcommand{\reffigurepage}[2]{\xspace[\ensuremath{\rhd}~\autoref{#1}{\color{fbbioblue} ,\,p.\pageref{#1}#2}]\xspace}
\newcommand{\reffiguresup}[2]{\xspace[\ensuremath{\rhd}~{\color{fbbioblue}Suppl.~}\autoref{#1}{\color{fbbioblue} #2}]\xspace}
\newcommand{\dns}{\xspace[\ensuremath{\rhd}~{\color{fbbioblue} data not shown}]\xspace}
\newcommand{\mip}{\xspace[\ensuremath{\rhd}~{\color{fbbioblue} manuscript in preparation}]\xspace}
\newcommand{\supple}{\xspace[\ensuremath{\rhd}~{\color{fbbioblue} supplement}]\xspace}
\newcommand{\supplefig}{\xspace[\ensuremath{\rhd}~{\color{fbbioblue} supplementary figure}]\xspace}
\newcommand{\reftable}[1]{\xspace[\ensuremath{\rhd}~\autoref{#1}]\xspace}
\newcommand{\reftablepage}[1]{\xspace[\ensuremath{\rhd}~\autoref{#1}, {\color{fbbioblue}p.}\pageref{#1}]\xspace}
\newcommand{\refeq}[1]{\xspace[\ensuremath{\rhd}~\autoref{#1}]\xspace}
\newcommand{\refeqpage}[1]{\xspace[\ensuremath{\rhd}~\autoref{#1}, {\color{fbbioblue}p.}\pageref{#1}]\xspace}
%%%%%%%% Config the new supplementary figure float %%%%%%%%%%%%%%
\floatstyle{plain}
\newfloat{figuresup}{h}{figsup}
\floatname{figuresup}{Suppl.~Fig}
%%%%%%% References %%%%%%%%%%%%%%%%
\newcommand{\dissref}[1]{\xspace[\ensuremath{\pmb\hookrightarrow}~\autoref{#1}]}
\newcommand{\dissrefpage}[1]{\xspace[\ensuremath{\pmb\hookrightarrow}~\autoref{#1}, {\color{fbbioblue}p.}\pageref{#1}]}
\newcommand{\citerev}[1]{\xspace[reviewed in~\citenum{#1}]}
\newcommand{\inlinerefpage}[1]{\autoref{#1} on page \pageref{#1}}
% % % Reference to outside content
\newcommand{\herestoyoufrank}[1]{
{\vspace{0.3em} \color{wwugray} \setlength{\fboxsep}{6pt}
\framebox[\textwidth][c]{
\begin{minipage}{0.2\textwidth}
\begin{center}
\includegraphics[width=2cm]{figures/output/raster/qr-thesismz.png}
\end{center}
{\tiny \raggedright Text abridged. Supplementary online information is available. \vfill}
\end{minipage}
\begin{minipage}{0.7\linewidth}
\footnotesize
\begin{itemize}
\setlength{\itemsep}{0pt}
\setlength{\parskip}{0pt}
\setlength{\parsep}{0pt}
#1
\end{itemize}
\end{minipage} \setlength{\fboxsep}{3pt}
}}
}
\newcommand{\fyfrank}{
{ \color{wwugray} \framebox[\textwidth][c]{
\setlength{\fboxsep}{6pt}
\begin{minipage}{0.95\textwidth}
\footnotesize \raggedright This section is printed in condensed form. Optionally, a version with additional information regarding methodical details and quality control is available as online supplement.
\end{minipage} \setlength{\fboxsep}{3pt}
}}
}
\newcommand{\supplebox}[1]{
{ \color{wwugray} \framebox[\textwidth][c]{
\setlength{\fboxsep}{6pt}
\begin{minipage}{0.95\textwidth}
\footnotesize \raggedright #1
\end{minipage} \setlength{\fboxsep}{3pt}
}}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%% ADDITIONAL SHORTHAND NOTATIONS %%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%% Typography %%%%%%%%%%
\newcommand{\typoplus}{\texttt{+}}
\newcommand{\typominus}{\texttt{-}}
%\newcommand{\myexp}[1]{\textperiodcentered10\textsuperscript{#1}}
\newcommand{\myexp}[1]{\num{1d#1} }
\newcommand{\ca}{Ca$^{2\text{+}}$\xspace}
\newcommand{\mgtwo}{Mg$^{2\text{+}}$\xspace} % Calcium Kation% Calcium Kation
\newcommand{\cak}{Ca$^{2\text{+}}$-concentration\xspace} % Calcium Konzentration
\newcommand{\plusmin}{\ensuremath{\stackrel{+}{\scriptstyle(\kern-1pt-\kern-1pt)}}}
%%%%%%%%%%%% Cell populations %%%%%%%%%%
\newcommand{\linneg}{Lin{\slshape \footnotesize -}\xspace}
\newcommand{\lsk}{Lin\textsuperscript{\slshape \footnotesize -} Sca\babelhyphen{nobreak}1\textsuperscript{\slshape \footnotesize +} c\babelhyphen{nobreak}Kit\textsuperscript{\slshape \footnotesize +}\xspace}
\newcommand{\lgmp}{Lin\textsuperscript{\slshape \footnotesize -} IL\babelhyphen{nobreak}7R\ensuremath{\alpha}\textsuperscript{\slshape \footnotesize +} Sca\babelhyphen{nobreak}1\textsuperscript{\slshape \footnotesize -} c\babelhyphen{nobreak}Kit\textsuperscript{\slshape \footnotesize +} CD34\textsuperscript{\slshape \footnotesize +} FC\ensuremath{\gamma}R\textsuperscript{\slshape \footnotesize +}\xspace}
\newcommand{\kit}{c\babelhyphen{nobreak}Kit\xspace}
\newcommand{\kitpos}{c\babelhyphen{nobreak}Kit\textsuperscript{\slshape \footnotesize +}\xspace}
\newcommand{\kithi}{c\babelhyphen{nobreak}Kit\textsuperscript{\slshape \footnotesize high}\xspace}
\newcommand{\kitlow}{c\babelhyphen{nobreak}Kit\textsuperscript{\slshape \footnotesize low}\xspace}
\newcommand{\cdelevenbpos}{CD11b{\slshape \footnotesize +}\xspace}
\newcommand{\cdonehundretseventeenpos}{CD117{\slshape \footnotesize +}\xspace}
%%%%%%%%%%%% Oncogenes %%%%%%%%%%%%%%
\newcommand{\mllfp}{MLL-FP\xspace}
\newcommand{\mllaffour}{MLL-AF4\xspace}
\newcommand{\mllafnine}{MLL-AF9\xspace}
\newcommand{\mllafninegfp}{MLL-AF9-{\scshape ires}-GFP\xspace}
\newcommand{\mycbcltwo}{MYC-BCL2\xspace}
%%%%%%%%%%%% Transcription factors %%%%%%%%%%%%%%
\newcommand{\tfcebpa}{\proteinnamehuman{C/EBP\ensuremath{\alpha}}}
\newcommand{\tfcebpb}{\proteinnamehuman{C/EBP\ensuremath{\beta}}}
\newcommand{\tfcebpg}{\proteinnamehuman{C/EBP\ensuremath{\gamma}}}
\newcommand{\tfcebpe}{\proteinnamehuman{C/EBP\ensuremath{\epsilon}}}
%%%%%%%%%%%%%%% Genes %%%%%%%%%%%%%%
\newcommand{\genename}[1]{#1\xspace}
\newcommand{\genenamehuman}[1]{{\uppercase\expandafter{#1}}\xspace}
\newcommand{\genenamemouse}[1]{#1\xspace}
\newcommand{\genenamedrosophila}[1]{#1\xspace}
%%%%%%%%%%%%%%% Protein %%%%%%%%%%%%%%
\newcommand{\proteinname}[1]{#1\xspace}
\newcommand{\proteinnamehuman}[1]{{\uppercase\expandafter{#1}}\xspace}
\newcommand{\proteinnamemouse}[1]{#1\xspace}
\newcommand{\proteinnamedrosophila}[1]{#1\xspace}
%%%%%%%%%%%%%%% Genotypes %%%%%%%%%%%%%%
\newcommand{\dnmtchipheadline}{Dnmt1\textsuperscript{ -/chip}\xspace}
\newcommand{\dnmtchip}{Dnmt1\textsuperscript{\slshape \footnotesize -/chip}\xspace}
\newcommand{\dnmtchipshort}{\textsuperscript{\slshape \footnotesize -/chip}\xspace}
\newcommand{\dnmtchipregular}{{\slshape \footnotesize -/chip}\xspace}
\newcommand{\dnmtfloxchip}{Dnmt1\textsuperscript{\slshape \footnotesize fl/chip}\xspace}
\newcommand{\dnmtcchip}{Dnmt1\textsuperscript{\slshape \footnotesize c/chip}\xspace}
\newcommand{\dnmtchipallele}{Dnmt1\textsuperscript{\slshape \footnotesize chip}-allele\xspace}
\newcommand{\dnmtcallele}{Dnmt1\textsuperscript{\slshape \footnotesize c}-allele\xspace}
\newcommand{\dnmtnallele}{Dnmt1\textsuperscript{\slshape \footnotesize n}-allele\xspace}
\newcommand{\dnmtnegallele}{Dnmt1\textsuperscript{\slshape \footnotesize -}-allele\xspace}
\newcommand{\dnmtwt}{Dnmt1\textsuperscript{\slshape \footnotesize +/+}\xspace}
\newcommand{\dnmtwtshort}{\textsuperscript{\slshape \footnotesize +/+}\xspace}
\newcommand{\dnmtwtregular}{{\slshape \footnotesize +/+}\xspace}
\newcommand{\cremx}{Mx1-Cre\xspace}
%%%%%%%%%%%%%%% Strains %%%%%%%%%%%%%%
\newcommand{\mmblsix}{C57BL/6\xspace}
\newcommand{\mmsvjae}{129/SvJae\xspace}
\newcommand{\mmsjlola}{SJL-Ola\xspace}
%%%%%%% HISTON MARKS %%%%%%%%%%%%%%%%
% in case we need a special formatting here
\newcommand{\histwoarg}{H3R2me2a\xspace}
\newcommand{\hisfourone}{H3K4me1\xspace}
\newcommand{\hisfourtwo}{H3K4me2\xspace}
\newcommand{\hisfourthree}{H3K4me3\xspace}
\newcommand{\hiseightac}{H3K8ac\xspace}
\newcommand{\hisnineac}{H3K9ac\xspace}
\newcommand{\hisninethree}{H3K9me3\xspace}
\newcommand{\hiseighteenac}{H3K18ac\xspace}
\newcommand{\hiseighteenub}{H3K18ub\xspace}
\newcommand{\histwentythreeub}{H3K23ub\xspace}
\newcommand{\histwentysevenac}{H3K27ac\xspace}
\newcommand{\histwentyseventwo}{H3K27me2\xspace}
\newcommand{\histwentyseventhree}{H3K27me3\xspace}
\newcommand{\histhirtysixtwo}{H3K36me2\xspace}
\newcommand{\histhirtysixthree}{H3K36me3\xspace}
\newcommand{\hisseventyninetwo}{H3K79me2\xspace}
\newcommand{\hisseventyninethree}{H3K79me3\xspace}
%%%%%%%%%%%% Other ChIP-targets %%%%%%%%%%%%%%%%%%
\newcommand{\poltwo}{RNA polymerase~{\uppercase \expandafter{\romannumeral2}}\xspace}
%%%%%%%%%%%% Enhancer clusters %%%%%%%%%%
\newcommand{\enhancerid}[2]{{\color{wwugray}\textbf{{\textsl{#1}:\tiny #2}}}\xspace}
\newcommand{\enhancertab}[2]{{#1:#2}\xspace}
\newcommand{\amitnum}[1]{\uppercase \expandafter{\romannumeral#1}\xspace}
\newcommand{\amitcluster}[2]{\textsl{#1}~({\uppercase \expandafter{\romannumeral#2}})\xspace}
\newcommand{\amitone}{\amitcluster{Common}{1}}
\newcommand{\amittwo}{\amitcluster{Myeloid\,+\,Progenitors}{2}}
\newcommand{\amittwon}{\amitcluster{Myeloid\,+\,Prog.}{2}}
\newcommand{\amitthree}{\amitcluster{Lymphoid\,+\,Progenitors}{3}}
\newcommand{\amitthreen}{\amitcluster{Lymphoid\,+\,Prog.}{3}}
\newcommand{\amitfour}{\amitcluster{Erythroid\,+\,Progenitors}{4}}
\newcommand{\amitfourn}{\amitcluster{Erythroid\,+\,Prog.}{4}}
\newcommand{\amitfive}{\amitcluster{Progenitors}{5}}
\newcommand{\amitsix}{\amitcluster{Myeloid}{6}}
\newcommand{\amitseven}{\amitcluster{B-cells}{7}}
\newcommand{\amiteight}{\amitcluster{TNK-cells}{8}}
\newcommand{\amitnine}{\amitcluster{Erythroid}{9}}
\newcommand{\amitten}{\amitcluster{Undefined}{10}}
\newcommand{\clade}[2]{\textsl{\uppercase \expandafter{\romannumeral#1}.#2}\xspace}
\newcommand{\cladesevenac}[2]{\textsl{\uppercase \expandafter{\romannumeral#1}.#2}{\footnotesize~(K27ac)}\xspace}
\newcommand{\cladefourthree}[2]{\textsl{\uppercase \expandafter{\romannumeral#1}.#2}{\footnotesize~(K4me3)}\xspace}
%%%%%%% TF motifs %%%%%%%%%%%%%%%%
\newcommand{\motif}[2]{{\color{wwugray}\textbf{{\textsl{#1}.\tiny #2}}}\xspace}
\newcommand{\motifnucleotides}[1]{{\color{wwugray}\textbf{\texttt{\large #1}}}\xspace}
\newcommand{\motifmlltwo}{\motif{DeNovo}{SSCGCGGCCTSS}}
\newcommand{\motifmlltwob}{\motif{DeNovo}{CGCCCCGCCCAC}}
\newcommand{\motifmlltwoc}{\motif{DeNovo}{CCGGRCGGCG}}
\newcommand{\motifx}{\motif{DeNovo}{CACTTCCTGT}}
\newcommand{\motifxb}{\motif{DeNovo}{TGACGTCACT}}
\newcommand{\motifxc}{\motif{DeNovo}{TTTCCCCWTTYG}}
\newcommand{\motifpolya}{\motif{DeNovo}{YAAAAAAAAV}}
\newcommand{\motifpuone}{{\color{wwugray}\textbf{\textsl{PU.1.ThioMac\-.{\tiny PU.1.ChIP.Seq.Homer}}}}\xspace}
\newcommand{\motifetsone}{{\color{wwugray}\textbf{\textsl{Ets1.like.CD4\-.{\tiny PolII.ChIP.Seq.Homer}}}}\xspace}
\newcommand{\motifcebpb}{{\color{wwugray}\textbf{\textsl{CEBP.CEBPb\-.{\tiny ChIP.Seq.Homer}}}}\xspace}
\newcommand{\motifetwoa}{{\color{wwugray}\textbf{\textsl{E2A.proBcell.E2A\-.{\tiny ChIP.Seq.Homer}}}}\xspace}
\newcommand{\motifmybb}{{\color{wwugray}\textbf{\textsl{MYB.HTH\-.{\tiny GSE22095}}}}\xspace}
\newcommand{\motifnanog}{{\color{wwugray}\textbf{\textsl{Nanog.Homeobox\-.{\tiny GSE11724}}}}\xspace}
\newcommand{\motifnkx}{{\color{wwugray}\textbf{\textsl{Nkx3.1.Homeobox\-.{\tiny GSE28264}}}}\xspace}
\newcommand{\motifrunx}{{\color{wwugray}\textbf{\textsl{RUNX.AML\-.{\tiny Runt.CD4}\xspace}}}\xspace}
\newcommand{\motifblh}{{\color{wwugray}\textbf{\textsl{SCL.bHLH\-.{\tiny GSE13511}\xspace}}}\xspace}
%%%%%%% Bioinformatic tools %%%%%%%%%%%%%%%%
\newcommand{\emphsoftwarename}[1]{\textsc{#1}}
\newcommand{\emphcollectionname}[1]{\textsc{#1}}
\newcommand{\emphdatabasename}[1]{\textsc{#1}}
\newcommand{\emphkeggname}[1]{\emph{#1}}
%%%%%%% Reference genomes %%%%%%%%%%%%%%%%
\newcommand{\mmnine}{\textsl{NCBI37/mm9}\xspace}
\newcommand{\mmten}{\textsl{GRCm38/mm10}\xspace}
\newcommand{\hgnineteen}{\textsl{GRCh37/hg19}\xspace}
%%%%%%%%%%%%%%% Chemicals %%%%%%%%%%%%%%
\newcommand{\polyic}{poly\,I:C\xspace}
%%%%%%% Other emphasis %%%%%%%%%%%%%%%%
\newcommand{\emphspecies}[1]{\emph{\slshape #1}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%% CV formatting %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand{\cvhead}[1]{\hskip-2mm\colorbox{fbbiolight}{
\hbox to\textwidth{
\fontsize{11.5pt}{13.2pt}\selectfont\color{white}
\hskip2mm\textbf{#1}
\vrule width0ptheight10ptdepth2pt\hss
}}}
\newcommand{\emphfrank}[1]{#1}