Skip to content
This repository has been archived by the owner on Dec 29, 2023. It is now read-only.

Commit

Permalink
Add batch corrected alpha-diversity (#18)
Browse files Browse the repository at this point in the history
  • Loading branch information
@Fumire
Fumire committed May 17, 2022
1 parent 376a3b3 commit 8959aed
Show file tree
Hide file tree
Showing 2 changed files with 58 additions and 12 deletions.
Binary file modified jwlee230/Report/presentation.pdf
View file
Binary file not shown.
70 changes: 58 additions & 12 deletions jwlee230/Report/presentation.tex
View file
Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@
\begin{itemize}
\item Greengenes (GG) \cite{greengenes1}
\item SILVA \cite{silva1, silva2}
\item Human Oral Microbiome Database (HOMD)
\item Human Oral Microbiome Database (HOMD) \cite{homd1}
\end{itemize}

“A \textbf{higher} performance at taxonomic levels above \textit{genus level}; \\
Expand Down Expand Up @@ -281,8 +281,9 @@
\end{figure}
\end{frame}

\subsection{Batch effect removal}
\begin{frame}
\frametitle{title}
\frametitle{t-SNE before \& after}
\end{frame}

\subsection{Diversity Index}
Expand All @@ -304,6 +305,51 @@
\begin{frame}[allowframebreaks]
\frametitle{Violin Plot with Alpha diversity}

\begin{figure}
$\begin{array}{cc}
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2.uncorrected/All+Data+faith_pd.pdf}
&
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2/All+Data+faith_pd.pdf}
\\
\mbox{(a) Uncorrected} & \mbox{(b) Corrected} \\
\end{array}$
\caption{Data \& Faith's PD}
\end{figure}

\begin{figure}
$\begin{array}{cc}
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2.uncorrected/All+Data+observed_otus.pdf}
&
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2/All+Data+observed_otus.pdf}
\\
\mbox{(a) Uncorrected} & \mbox{(b) Corrected} \\
\end{array}$
\caption{Data \& Observed OTUs}
\end{figure}

\begin{figure}
$\begin{array}{cc}
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2.uncorrected/All+Data+pielou_e.pdf}
&
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2/All+Data+pielou_e.pdf}
\\
\mbox{(a) Uncorrected} & \mbox{(b) Corrected} \\
\end{array}$
\caption{Data \& Pielou Evenness}
\end{figure}

\begin{figure}
$\begin{array}{cc}
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2.uncorrected/All+Data+shannon.pdf}
&
\includegraphics[width=0.4 \linewidth]{figures/AlphaDiversity/everything.DADA2/All+Data+shannon.pdf}
\\
\mbox{(a) Uncorrected} & \mbox{(b) Corrected} \\
\end{array}$
\caption{Data \& Shannon Entropy}
\end{figure}


\begin{figure}
$\begin{array}{ccc}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+faith_pd.pdf}
Expand All @@ -319,24 +365,24 @@

\begin{figure}
$\begin{array}{ccc}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+observed_features.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+observed_otus.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+observed_features.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+observed_otus.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+observed_features.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+observed_otus.pdf}
\\
\mbox{(a) Mother Mouth} & \mbox{(b) Neonate 3-day} & \mbox{(c) Neonate 5-day} \\
\end{array}$
\caption{Detail premature \& Observed Features}
\caption{Detail premature \& Observed OTUs}
\end{figure}

\begin{figure}
$\begin{array}{ccc}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+pielou_evenness.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+pielou_e.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+pielou_evenness.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+pielou_e.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+pielou_evenness.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+pielou_e.pdf}
\\
\mbox{(a) Mother Mouth} & \mbox{(b) Neonate 3-day} & \mbox{(c) Neonate 5-day} \\
\end{array}$
Expand All @@ -345,11 +391,11 @@

\begin{figure}
$\begin{array}{ccc}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+shannon_entropy.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Mouth+Detail_Premature+shannon.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+shannon_entropy.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-3day+Detail_Premature+shannon.pdf}
&
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+shannon_entropy.pdf}
\includegraphics[width=0.3 \linewidth]{figures/AlphaDiversity/everything.DADA2/Neonate-5day+Detail_Premature+shannon.pdf}
\\
\mbox{(a) Mother Mouth} & \mbox{(b) Neonate 3-day} & \mbox{(c) Neonate 5-day} \\
\end{array}$
Expand Down

0 comments on commit 8959aed

Please sign in to comment.