ENH integrate tables and figs into aim 3

tables/mouse_dose_car.tex

@@ -1,7 +1,7 @@
-\begin{tabular}{lcc} 
+\begin{tabular}{lccc} 
 \\[-1.8ex]\hline 
 \hline \\[-1.8ex] 
-\\[-1.8ex] & Dose & 1e6 T cells/mouse & 1e6 CAR T cells/mouse 1e6 (DMS) & CAR T cells/mouse (Bead) \\ 
+\\[-1.8ex] Dose & 1e6 T cells/mouse & 1e6 CAR T cells/mouse 1e6 (DMS) & CAR T cells/mouse (Bead) \\ 
 \hline \\[-1.8ex] 
 High & 1.25 & 0.855 & 0.315 \\
 Medium & 0.8325 & 0.570 & 0.210 \\

tex/thesis.tex

@@ -1603,18 +1603,130 @@ between survival groups.
 \subsection{DMS-expanded T cells show greater anti-tumor activity \invivo{}
   compared to beads}
 
-% figure showing the experimental model and dosing strategy
+\begin{figure*}[ht!]
-% table for % CAR+ T cells injected into the mice
+  \begingroup
-% figure for the mem and CAR+ percent injected into the mice
+
-% figure showing IVIS images
+  \includegraphics{../figures/mouse_dosing_overview.png}
-% figure showing the surival curves
+
+  \endgroup
+  \caption[Mouse Dosing Experimental Overview]
+  {Overview of \invivo{} experiment to test \gls{car} T cells expanded with
+    either \glspl{dms} at different doses. }
+  \label{fig:mouse_dosing_overview}
+\end{figure*}
+
+
+\begin{table}[!h] \centering
+  \caption{Results for \gls{car} T cell \invivo{} dose study}
+  \label{tab:mouse_dosing_results}
+  \input{../tables/mouse_dose_car.tex}
+\end{table}
+
+% TODO put growth first in this figure
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/mouse_dosing_qc.png}
+  \phantomsubcaption\label{fig:mouse_dosing_qc_mem}
+  \phantomsubcaption\label{fig:mouse_dosing_qc_cd4}
+  \phantomsubcaption\label{fig:mouse_dosing_qc_growth}
+
+  \endgroup
+  \caption[Mouse Dosing T cell Characteristics]
+  {Characteristics of T cells harvested at day 14 injected into NSG
+    mice at varying doses.
+    Fractions of T cell subtypes in the day 14 product including
+    \subcap{fig:mouse_dosing_qc_mem}{\ptmemp{}}.
+    \subcap{fig:mouse_dosing_qc_cd4}{\pthp{}}, and
+    \subcap{fig:mouse_dosing_qc_growth}{Fold change of T cells.}
+  }
+  \label{fig:mouse_dosing_qc}
+\end{figure*}
+
+% TODO explain what statistical test was used here
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/mouse_dosing_ivis.png}
+  \phantomsubcaption\label{fig:mouse_dosing_ivis_images}
+  \phantomsubcaption\label{fig:mouse_dosing_ivis_plots}
+  \phantomsubcaption\label{fig:mouse_dosing_ivis_survival}
+  \phantomsubcaption\label{fig:mouse_dosing_ivis_survival_comp}
+
+  \endgroup
+  \caption[Mouse Dosing IVIS and Survival Results]
+  {T cells expanded with \glspl{dms} confer greater anti-tumor potency \invivo{}
+    even at lower doses.
+    \subcap{fig:mouse_dosing_ivis_images}{IVIS images of Nalm-6 tumor-bearing
+      \gls{nsg} mice injected with varying doses of T cells}
+    \subcap{fig:mouse_dosing_ivis_plots}{Plots showing quantified photon counts
+      of the results from (\subref{fig:mouse_dosing_ivis_plots}).}
+    \subcap{fig:mouse_dosing_ivis_survival}{Survival plots of mice}
+    \subcap{fig:mouse_dosing_ivis_survival_comp}{Survival plots of mice showing
+      only those that received a comparable number of \gls{car} T cells.}
+  }
+  \label{fig:mouse_dosing_ivis}
+\end{figure*}
 
 \subsection{Beads and DMSs perform similarly at earlier timepoints}
 
-% figure showing the experimental model and dosing strategy
+\begin{figure*}[ht!]
-% figure for the mem and CAR+ percent injected into the mice
+  \begingroup
-% figure showing IVIS images
+
-% figure showing the photon plots per time
+  \includegraphics{../figures/mouse_timecourse_overview.png}
+
+  \endgroup
+  \caption[Mouse Timecourse Experimental Overview]
+  {Overview of \invivo{} experiment to test \gls{car} T cells using either
+    \glspl{dms} or bead harvested at varying timepoints.
+  }
+  \label{fig:mouse_timecourse_overview}
+\end{figure*}
+
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/mouse_timecourse_qc.png}
+  \phantomsubcaption\label{fig:mouse_timecourse_qc_growth}
+  \phantomsubcaption\label{fig:mouse_timecourse_qc_car}
+  \phantomsubcaption\label{fig:mouse_timecourse_qc_cd4}
+  \phantomsubcaption\label{fig:mouse_timecourse_qc_mem}
+
+  \endgroup
+  \caption[Mouse Timecourse T cell Characteristics]
+  {Characteristics of T cells harvested at varying timepoints injected into NSG
+    mice.
+    \subcap{fig:mouse_timecourse_qc_growth}{Fold change of T cells (each
+      timepoint only includes the runs that were harvested at day 14).}
+    Fractions of T cell subtypes in the day 14 product including
+    % TODO refactor CAR+ percent into nice macro
+    \subcap{fig:mouse_timecourse_qc_car}{\gls{car}+~\si{\percent}},
+    \subcap{fig:mouse_timecourse_qc_cd4}{\pthp{}}, and
+    \subcap{fig:mouse_timecourse_qc_mem}{\ptmemp{}}.
+  }
+  \label{fig:mouse_timecourse_qc}
+\end{figure*}
+
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/mouse_timecourse_ivis.png}
+  \phantomsubcaption\label{fig:mouse_timecourse_ivis_images}
+  \phantomsubcaption\label{fig:mouse_timecourse_ivis_plots}
+
+  \endgroup
+  \caption[Mouse Timecourse IVIS Results]
+  {\glspl{dms} exhibit superior anti-tumor activity \invivo{} at day 14 compared
+    to beads but are similar to beads at lower timepoints.
+    \subcap{fig:mouse_timecourse_ivis_images}{IVIS images for day 6 to day 42 of
+    mice treated with varying doses of \gls{car} T cells grown with beads or
+    \glspl{dms}.}
+    \subcap{fig:mouse_timecourse_ivis_plots}{Quantified dotplots of the images
+      in (\subref{fig:mouse_timecourse_ivis_images}). Numbers beneath each dot
+      represent the number of mice at that timepoint.},
+  }
+  \label{fig:mouse_timecourse_ivis}
+\end{figure*}
 
 \section{discussion}