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Posts tagged “scatterplot matrix

Discriminating Between Iris Species

The Iris data set is a famous for its use to compare unsupervised classifiers.

The goal is to use information about flower characteristics to accurately classify the 3 species of Iris. We can look at scatter plots of the 4 variables in the data set and see that no single variable nor bivariate combination can achieve this.

One approach to improve the separation between the two closely related Iris species, I.versicolor (blue) and I.virginica (green), is to use a combination of all 4 measurements, by constructing principal components (PCs).

Using the singular value decomposition to calculate PCs we see that the sample scores above are not resolved for the two species of interest.

Another approach is to use a supervised projection method like partial least squares (PLS), to identify Latent Variables (LVs) which are data projections similar to those of PCA, but  which are also correlated with the species label. Interestingly this approach leads to a projection which changes the relative orientation of  I. versicolor and I. verginica to I. setaosa. However,  this supervised approach is not enough to identify a hyperplane of separation between all three species.

Non-linear PCA via neural networks can be used to identify the hypersurface of separation, shown above. Looking at the scores we can see that  this  approach is the most success for resolving the  two closely related species. However, the loadings from this method, which help relate how the variables are combined achieve the classification, are impossible to interpret. In the case of the function used above(nlPca, pcaMethods R package)  the loadings are literally NA.


Visualizing the Iris Data

I’ve been working on additional scatter plot matrix plotting capabilities for the imCorrelations module.

Here is a little preview of a modified gpairs function from the YaleToolkit R package which is used to visualize the Iris data set. This scatterplot matrix allows for many interesting combinations of plots, which can be annotated with colors based on categorical variable(s).

The upper and lower matrix triangles can be modified with a variety of inputs:

  • scatterplots: points, best-fit-line, loess, qqplot for linear model residuals, best-fit-line confidence interval, correlation statistics
  • conditional plots: boxplot, stripplot, barcode

    Scatterplot matrix for overview of correlations and regressions, displaying box plots for Iris data species, variable histograms, correlation statistics, stripcharts and best fit lines.

This can be easily modified to rapidly visualize and overview variable dependencies.

Displaying Iris data, confidence intervals for best fit lines, residual quantile-quantile plots and variable barcode plots.