Multidimensional Scaling (MDS) is a powerful statistical method that can be effectively used to elucidate hidden population structure, and more importantly, use it as a quality control tool while working on genetic data.
Note: I strongly encourage anyone to QC their data (phenotype or genotype data) before proceeding to any further data analysis. In my own research, I work with plethora of genetic data genetrated from the breeding programs, and I use MDS religiously to identify any possible pollen contamination (selfed or out-crossess), and or mislabled samples, and further, I use it as a population structure covariates in GLM and MLM in GWAS analysis.
In this tutorial, I will walk through how anyone can use easily run MDS analysis on their data in
TASSEL software and visualize in
R software. For detail information on MDS, please read this article at this link
What is MDS?
MDS is also known as
Prinicpal Co-ordinate Analysis (PCoA), and produces results that are very similar to
Principal Component Analysis (PCA). A genome-wide pairwise
Identity-By-State (IBS) distance matrix using the genotype data is first calculated, then following the MDS analysis.
In this tutorial, I will show how to calculate MDS in
TASSEL software. If you are familiar with TASSEL or do not have it installed on your computer, then, please download and go through its documentation at this link .
Step: 1 Import data in TASSEL
Step: 2 Calculate distance matrix
Step: 3 Calculate MDS
Step: 4 Plot PCoAs in TASSEL
Optional step: Plotting in R using ggplot2
MDS results as a
.txt file and edit in
MS Excel to add the below
header and information to plot in
Once the file has bee formatted, One may plot the PCoA results using
ggplot2 library in
R software using the below commands:
#Library library(ggplot2) #import MDS data MDS = read.table("MDS.txt", header = T) head(MDS) #Plot MDS MDS_plot <- ggplot(MDS, aes(x=PC1,y=PC2,color=Type, cex=1, label=Sample)) MDS_plot <- MDS_plot + geom_point() + geom_text(aes(label=Sample),hjust=0, vjust=0) MDS_plot
An example of an ouptut from the
R command is shown below. In the figure below, the samples represent PCoA of samples from a F1 cross, and one may see that most of the F1 progenies cluster between the parent clusters on the left and right, whereas, there are a few samples (in circle) that cluster with one of the parents indicating that they were a self-pollinated.
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Thank you for reading this tutorial. If you have any questions or comments, please let me know in the comment section below or send me an email.
Happy QC-ing !
Bradbury, Peter J., et al. "TASSEL: software for association mapping of complex traits in diverse samples." Bioinformatics 23.19 (2007): 2633-2635.
Tzeng, Jengnan, Henry Horng-Shing Lu, and Wen-Hsiung Li. "Multidimensional scaling for large genomic data sets." BMC bioinformatics 9.1 (2008): 179.