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Comparison between Principal Coordinate Analysis (PCoA) and Principal Component

Analysis (PCA)

Principal coordinates analysis (PCoA) is another eigen-based method which is quite similar to
PCA in reducing dimensionality by projecting multidimensional sets of data into a smaller
number of dimensions (Gower, 1966; Zuur et al., 2007; Huntley, 2011). The axes for both
analyses are plotted against each other in euclidean space. Both PCoA and PCA required set
of data without missing values in order to carry out the analysis. Principal Coordinate
Analysis (PCoA) is sometime referring as metric multidimensional scaling (MDS) or classical
There are several characteristics that allowed the PCoA to be distinguished from PCA. For
instance, PCoA and PCA can be easily recognized with their respective type of analysis mode
which includes R- mode and Q- mode. The R- mode analysis focus on the relationship among
the variables, meanwhile, Q-mode analysis focus on the association between individual
observations in a data set. PCA is an R-mode analysis, which analyze the matrix based on
similarities e.g. correlation or covariance. PCoA, on the other hand, is Q- mode analysis which
use dissimilarities coefficient (Hammer and Harper, 2006; Reyment, 1991). The PCoA also
has less stringent assumptions as compare to PCA. The PCoA can works with continuous
variables, discontinuous variables, ranked variables, attribute variables, or any combination
(Huntley, 2011).

Moreover, in PCA the data undergo a rigid rotation, but in PCoA, the relative distances
between data points are preserved as close as possible. The two-dimensional projection of
PCA and PCoA are shown in Fig. 1A and 1B, respectively. PCA is a projection of samples
onto a new set of axes, where the maximum variance is projected along the first axis, the
variance that not correlated with this axis is projected into another axis. On the other ha nd,
PCoA permits the positioning of the objects in a space of reduced dimensionality, while
preserving their distance relationship as close as possible. Furthermore, PCoA also does not
produce bi-plot (a joint plot of the variables and observations).

Figure 1. (A) PCA projection points on the axes with 3 species, and (B) PCoA samples
projection connected by distances.

Sometime PCoA will produce negative eigenvalues which are typically associated with
variance (Hammer and Harper, 2006). The PCoA also produce only estimate of the original
distances between points, therefore, interpreting the ordination in terms of the original
variables are problematic. PCoA have an advantage over PCA, since it can use any measure
of association (Zuur et al. 2007). For instance, if we have a set data with 400 observations
(percentage cover) and 20 weed families, however, many of the observations equal to zero
and various species have a patchy distribution. This situation makes the correlation and
covariance coefficients in PCA to be less appropriate tools to define association. Therefore,
PCoA can be used to tell us how dissimilar the families are and give us the required graphical

Gower, J.C. (1966). Some distance properties of latent root and vector methods used in
multivariate analysis. Biometrika, 53, 325-338.

Hammer, . and Harper, D.A.T. (2006). Paleontological data analysis. Oxford: Blackwell.

Huntley, J.W. (2011). Exploratory multivariate techniques and their utility for understanding
ancient ecosystem. In Quantifiying the Evolution of Early Life, (eds.) Laflamme et al.
New York: Springer.

Reyment, R.A. (1991). Multidimensional paleobiology. Oxford: Pergamon.

Zuur, A.F., Leno, E.N. and Smith, G.M. (2007). Statistics for Biology and Health: Statistics
for Biology and Health. New York: Springer.