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A scatter plot, also called a scatterplot, scatter graph, scatter chart, scattergram, or scatter diagram, [2] is a type of plot or mathematical diagram using Cartesian coordinates to display values for typically two variables for a set of data. If the points are coded (color/shape/size), one additional variable can be displayed.
Matplotlib (portmanteau of MATLAB, plot, and library [3]) is a plotting library for the Python programming language and its numerical mathematics extension NumPy.It provides an object-oriented API for embedding plots into applications using general-purpose GUI toolkits like Tkinter, wxPython, Qt, or GTK.
Scagnostics (scatterplot diagnostics) is a series of measures that characterize certain properties of a point cloud in a scatter plot. The term and idea was coined by John Tukey and Paul Tukey, though they didn't publish it; later it was elaborated by Wilkinson, Anand, and Grossman. The following nine dimensions are considered: [1] [2]
While t-SNE plots often seem to display clusters, the visual clusters can be strongly influenced by the chosen parameterization (especially the perplexity) and so a good understanding of the parameters for t-SNE is needed. Such "clusters" can be shown to even appear in structured data with no clear clustering, [13] and so
DBSCAN optimizes the following loss function: [10] For any possible clustering = {, …,} out of the set of all clusterings , it minimizes the number of clusters under the condition that every pair of points in a cluster is density-reachable, which corresponds to the original two properties "maximality" and "connectivity" of a cluster: [1]
The average silhouette of the data is another useful criterion for assessing the natural number of clusters. The silhouette of a data instance is a measure of how closely it is matched to data within its cluster and how loosely it is matched to data of the neighboring cluster, i.e., the cluster whose average distance from the datum is lowest. [8]
Multidimensional scaling (MDS) is a means of visualizing the level of similarity of individual cases of a data set. MDS is used to translate distances between each pair of objects in a set into a configuration of points mapped into an abstract Cartesian space.
The method consists of plotting the explained variation as a function of the number of clusters and picking the elbow of the curve as the number of clusters to use. The same method can be used to choose the number of parameters in other data-driven models, such as the number of principal components to describe a data set.