From 8ea9b8f4caa5f1a09a3e63e785612cb0865369cb Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Fri, 23 Jul 2021 17:34:04 -0400
Subject: [PATCH] ENH integrate expansion figure

---
 tex/thesis.tex | 37 ++++++++++++++++++++++++++++++++++---
 1 file changed, 34 insertions(+), 3 deletions(-)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index eb9c75c..83996ef 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -123,6 +123,10 @@
 \newcommand{\cdp}[1]{\pos{\cd{#1}}}
 \newcommand{\cdn}[1]{\cd{#1}-}
 \newcommand{\ptmem}{\cdp{62L}\pos{CCR7}}
+\newcommand{\pth}{\cdp{4}}
+\newcommand{\ptk}{\cdp{8}}
+\newcommand{\ptmemh}{\pth\ptmem}
+\newcommand{\ptmemk}{\ptk\ptmem}
 
 \newcommand{\catnum}[2]{(#1, #2)}
 \newcommand{\product}[3]{#1 \catnum{#2}{#3}}
@@ -977,7 +981,7 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
   \phantomsubcaption\label{fig:dms_cells_fluor}
 
   \endgroup
-  \caption[\gls{dms} Reaction timing]
+  \caption[T cells growing on \glspl{dms}]
   {Cells grow in tight clusters in and around functionalized \gls{dms}.
     \subcap{fig:dms_cells_phase}{Phase-contrast image of T cells growing on
       \glspl{dms} on day 7}
@@ -985,14 +989,41 @@ context of pure error). Statistical significance was evaluated at $\upalpha$ =
       growing on \glspl{dms} on day 9. \Glspl{dms} were stained using
       \gls{stppe} (red) and T cells were stained using \acd{45}-\gls{af647}.}
   }
-  \label{fig:dms_flowchart}
+  \label{fig:dms_cells}
 \end{figure*}
 
 % 3-donor expansion figure
 
 \subsection{DMSs lead to greater expansion and memory and CD4+ phenotypes}
 
-% phenotype expansion plots
+% TODO add significance tests to this
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/dms_vs_bead_expansion.png}
+  \phantomsubcaption\label{fig:dms_exp_fold_change}
+  \phantomsubcaption\label{fig:dms_exp_mem}
+  \phantomsubcaption\label{fig:dms_exp_cd4}
+  \phantomsubcaption\label{fig:dms_exp_mem4}
+  \phantomsubcaption\label{fig:dms_exp_mem8}
+
+  \endgroup
+  \caption[\gls{dms} vs bead expansion]
+  {\gls{dms} lead to superior expansion of T cells compared to beads across
+    multiple donors.
+    \subcap{fig:dms_exp_fold_change}{Longitudinal fold change of T cells grown
+      using either \glspl{dms} or beads. Significance was evaulated using t
+      tests at each timepoint}
+    Fold change of subpopulations expanded using either \gls{dms} or beads at
+    day 14, including 
+    \subcap{fig:dms_exp_mem}{\ptmem{} cells},
+    \subcap{fig:dms_exp_cd4}{\pth{} cells},
+    \subcap{fig:dms_exp_mem4}{\ptmemh{} cells}, and
+    \subcap{fig:dms_exp_mem8}{\ptmemk{} cells}
+  }
+  \label{fig:dms_exp}
+\end{figure*}
+
 % phenotype flow plots
 
 \subsection*{DMSs can be used to produce functional CAR T cells}