Questions tagged [biplot]

Biplot or dual plot is an exploratory graph to present - as points or vectors - both the observations (sample) and the variables of the data. The axes are typically latent principal dimensions. Biplot is often used to depict principal component analysis, correspondence analysis, and other multivariate methods.

Biplot is an exploratory graph to present both the data points (sample) and the variables. There are several variations, and the mostly used version is the biplot for principal components.

The original matrix $X$ (dimension $n \times p$, $n$ observations, $p$ variables) is transformed to $Y$ by centering and/or standardizing the columns. Using the singular value decomposition (SVD), we can write $$Y = UDV^T=\sum_{k=1,...p}d_k\mathbf u_k\mathbf v_k^T,$$ where the $\mathbf u_k$ are $n$-dimensional column vectors, the $\mathbf v_k$ are $p$-dimensional column vectors, and the $d_k$ are a non-increasing sequence of non-negative scalars. The biplot is formed from two scatterplots that share a common set of axes and have a between-set scalar product interpretation. The first scatterplot is formed from the points ($d_1^\alpha u_{1i}, d_2^\alpha u_{2i}$), for $i = 1,...,n$. The second plot is formed from the points ($d_1^{1-\alpha}v_{1j}, d_2^{1-\alpha}v_{2j}$), for $j = 1,...,p$. The $\alpha$ can be set as 0, 0.5, or 1. [Wikipedia]

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PCA and Correspondence analysis in their relation to Biplot

Biplot is often used to display results of principal component analysis (and of related techniques). It is a dual or overlay scatterplot showing component loadings and component scores simultaneously. I was informed by @amoeba today that he has…
ttnphns
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Interpretation of biplots in principal components analysis

I came across this nice tutorial: A Handbook of Statistical Analyses Using R. Chapter 13. Principal Component Analysis: The Olympic Heptathlon on how to do PCA in R language. I don't understand the interpretation of Figure 13.3: So I am plotting…
user862
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Visualizing a million, PCA edition

Is it possible to visualize the output of Principal Component Analysis in ways that give more insight than just summary tables? Is it possible to do it when the number of observations is large, say ~1e4? And is it possible to do it in R [other…
gappy
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What are the four axes on PCA biplot?

When you construct a biplot for a PCA analysis, you have principal component PC1 scores on the x-axis and PC2 scores on the y-axis. But what are the other two axes to the right and the top of the screen?
Nils
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Interpreting 2D correspondence analysis plots

I've been searching the internet far and wide... I have yet to find a really good overview of how to interpret 2D correspondence analysis plots. Could someone offer some advice on interpreting the distances between points? Perhaps an example would…
Brandon Bertelsen
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Positioning the arrows on a PCA biplot

I am looking to implement a biplot for principal component analysis (PCA) in JavaScript. My question is, how do I determine the coordinates of the arrows from the $U,V,D$ output of the singular vector decomposition (SVD) of the data matrix? Here is…
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What is the proper association measure of a variable with a PCA component (on a biplot / loading plot)?

I am using FactoMineR to reduce my data set of measurements to the latent variables. The variable map above is clear for me to interpret, but I am confused when it comes to the associations between the variables and component 1. Looking at the…
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What do the arrows in a PCA biplot mean?

Consider the following PCA biplot: library(mvtnorm) set.seed(1) x <- rmvnorm(2000, rep(0, 6), diag(c(5, rep(1,5)))) x <- scale(x, center=T, scale=F) pc <- princomp(x) biplot(pc) There are a bunch of red arrows plotted, what do they mean? I knew…
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What is the difference between "loadings" and "correlation loadings" in PCA and PLS?

One common thing to do when doing Principal Component Analysis (PCA) is to plot two loadings against each other to investigate the relationships between the variables. In the paper accompanying the PLS R package for doing Principal Component…
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Can the scaling values in a linear discriminant analysis (LDA) be used to plot explanatory variables on the linear discriminants?

Using a biplot of values obtained through principal component analysis, it is possible to explore the explanatory variables that make up each principle component. Is this also possible with Linear Discriminant Analysis? Examples provided use the…
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How to interpret this PCA biplot coming from a survey of what areas people are interested in?

Background: I asked hundreds of participants in my survey how much they are interested in selected areas (by five point Likert scales with 1 indicating "not interested" and 5 indicating "interested"). Then I tried PCA. The picture below is a…
sitems
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Arrows of underlying variables in PCA biplot in R

At the risk of making the question software-specific, and with the excuse of its ubiquity and idiosyncrasies, I want to ask about the function biplot() in R, and, more specifically, about the calculation and plotting of its default, superimposed red…
Antoni Parellada
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Data space, variable space, observation space, model space (e.g. in linear regression)

Suppose we have the data matrix $\mathbf{X}$, which is $n$-by-$p$, and the label vector $Y$, which is $n$-by-one. Here, each row of the matrix is an observation, and each column corresponds to a dimension/variable. (assume $n>p$) Then what do data…
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Variable ordering using PCA

I've downloaded a script to draw a correlation matrix using colored circles. This script allows to order variables using PCA, but I'm not sure how it works. The code responsible for ordering is below: if (order) { if(!n==m){ …
Tomek Tarczynski
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Interpretation of biplot in PCA

Blue points all appear in the lower right-hand quadrant in the plane formed by the first two principal components. Is it a good interpretation of the biplot (right panel) to say that blue points are mainly characterized by large values of X1 and…
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