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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.
Moreover, complementary Python packages are available; SciPy is a library that adds more MATLAB-like functionality and Matplotlib is a plotting package that provides MATLAB-like plotting functionality. Although matlab can perform sparse matrix operations, numpy alone cannot perform such operations and requires the use of the scipy.sparse library.
CuPy is an open source library for GPU-accelerated computing with Python programming language, providing support for multi-dimensional arrays, sparse matrices, and a variety of numerical algorithms implemented on top of them. [3] CuPy shares the same API set as NumPy and SciPy, allowing it to be a drop-in replacement to run NumPy/SciPy code on GPU.
|border= Whether of not to show the border (default yes) |yx= Take y then x instead of x then y (default no) |color-even= Sets every other dot to a specific color (default red) |color-odd= Sets every odd dot to a specific color (default red) |square= Makes the chart/plot a square (default no) |width= The width of the chart
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
SymPy is an open-source Python library for symbolic computation. It provides computer algebra capabilities either as a standalone application, as a library to other applications, or live on the web as SymPy Live [2] or SymPy Gamma. [3] SymPy is simple to install and to inspect because it is written entirely in Python with few dependencies.
scikit-learn (formerly scikits.learn and also known as sklearn) is a free and open-source machine learning library for the Python programming language. [3] It features various classification, regression and clustering algorithms including support-vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with the Python numerical and scientific ...
DOT graphs are typically stored as files with the .gv or .dot filename extension — .gv is preferred, to avoid confusion with the .dot extension used by versions of Microsoft Word before 2007. [1] dot is also the name of the main program to process DOT files in the Graphviz package. Various programs can process DOT files.