-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathSupplementary_Information.tex
104 lines (84 loc) · 3.83 KB
/
Supplementary_Information.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
\documentclass[12pt, letterpaper]{article}
\usepackage[utf8]{inputenc}
\usepackage[margin=1in]{geometry}
\usepackage[super]{nth}
\usepackage{hyperref}
\usepackage{lineno}
\usepackage[
singlelinecheck=false
]{caption}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{bm}
\usepackage{bbm}
\usepackage{graphicx}
\usepackage{csvsimple}
\usepackage[section]{placeins}
\usepackage{lineno}
\usepackage{natbib}
\title{A joint framework for the estimation of PCA and F-statistics using ancient DNA}
\author{Divyaratan Popli, Benjamin M. Peter}
%\date{5 August 2021}
\linenumbers
\setlength{\parskip}{1em}
\setlength{\parindent}{0em}
\newcommand{\BZ}{\mathbf{Z}}
\newcommand{\BD}{\mathbf{D}}
\newcommand{\BN}{\mathbf{N}}
\newcommand{\BH}{\mathbf{H}}
\newcommand{\Btheta}{\pmb{\theta}}
\begin{document}
\maketitle
%\renewcommand\thefigure{\arabic{figure}}
\section*{Supplementary Figures}
%\setcounter{figure}{0}
\renewcommand{\figurename}{Fig S}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/pcplot2.png}
\centering
\caption{Variation in the genetic data explained with the top 10 PCs from PPCA. Each panel shows the position of individuals on a Principal Component. Jitter is added to y-axis to show the data points clearly. The last 2 PCs explain $0\%$ variation because the PPCA model with scale=8 explicitly sets the non- relevant PCs to 0.}
\label{figS1:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/pcaplot2.png}
\centering
\caption{Variation in the genetic data explained with the top 10 PCs from classical PCA. Each panel shows the position of individuals on a Principal Component. Jitter is added to y-axis to show the data points clearly.}
\label{figS1:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/lseplot2.png}
\centering
\caption{Variation in the genetic data explained with the top 10 PCs from LSE. Each panel shows the position of individuals on a Principal Component. Jitter is added to y-axis to show the data points clearly.}
\label{figS1:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/lse_admix.png}
\centering
\caption{$f_2(X_1,X_4)$ estimated with LSE converges to the estimate from ADMIXTOOLS 2, when all PCs are used.}
\label{figS1:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/mu0.05_plot_all.png}
\centering
\caption{Comparison of PPCA and LSE to ADMIXTOOLS 2 using genotypes from ten individuals in each population. Top panel shows $F_2$ estimates for different populations, and the bottom left and right panels show estimates for $F_3$ and $F_4$ respectively.}
\label{figS2:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/mu0.05_plot_all_1ind.png}
\centering
\caption{Comparison of PPCA and LSE to ADMIXTOOLS 2 using genotypes from one individual from each population. Top panel shows $F_2$ estimates for different individuals, and the bottom left and right panels show estimates for $F_3$ and $F_4$ respectively.}
\label{figS2:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/hypothesis_test_comparison.png}
\centering
\caption{Test for admixture with F4 statistic. We compare ADMIXTOOLS 2 (orange)to PPCA-based-framework (blue). Horizontal dashed lines denote 2 and 3 standard deviations from the mean.}
\label{figS2:pc_scale}
\end{figure}
\begin{figure}[ht!]
\includegraphics[width=16.5cm]{Images/Supplement/f2_f3_corr_x1.png}
\centering
\caption{Comparison of f3(Altai ; Vindija33.19, Vindija87) with f2(Altai, Vindija33.19) (shown in dashed lines) estimated with ADMIXTOOLS 2 and PPCA with 8 PCs.}
\label{figS2:pc_scale}
\end{figure}
\end{document}