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plot_semivariogram.py – Fits a model between two distance matrices and plots the result

Description:

Fits a spatial autocorrelation model between two matrices and plots the result. This script will work with two distance matrices but will ignore the 0s at the diagonal and the values that go to N/A

Usage: plot_semivariogram.py [options]

Input Arguments:

Note

[REQUIRED]

-x, --input_path_x
Path to distance matrix to be displayed in the x axis
-y, --input_path_y
Path to distance matrix to be displayed in the y axis
-o, --output_path
Output path. directory for batch processing, filename for single file operation

[OPTIONAL]

-b, --binning
Binning ranges. Format: [increment,top_limit], when top_limit is -1=infinitum; you can specify several ranges using the same format, i.e. [2.5,10][50,-1] will set two bins, one from 0-10 using 2.5 size steps and from 10-inf using 50 size steps. Note that the binning is used to clean the plots (reduce number of points) but ignored to fit the model. [default: None]
--ignore_missing_samples
This will overpass the error raised when the matrices have different sizes/samples
--x_max
X axis max limit [default: auto]
--x_min
X axis min limit [default: auto]
--y_max
Y axis max limit [default: auto]
--y_min
Y axis min limit [default: auto]
-X, --x_label
Label for the x axis [default: Distance Dissimilarity (m)]
-Y, --y_label
Label for the y axis [default: Community Dissimilarity]
-t, --fig_title
Title of the plot [default: Semivariogram]
--dot_color
Dot color for plot, more info: http://matplotlib.sourceforge.net/api/pyplot_api.html [default: white]
--dot_marker
Dot color for plot, more info: http://matplotlib.sourceforge.net/api/pyplot_api.html [default: o]
--line_color
Line color for plot, more info: http://matplotlib.sourceforge.net/api/pyplot_api.html [default: blue]
--dot_alpha
Alpha for dots, more info: http://matplotlib.sourceforge.net/api/pyplot_api.html [default: 1]
--line_alpha
Alpha for dots, more info: http://matplotlib.sourceforge.net/api/pyplot_api.html [default: 1]
-m, --model
Model to be fitted to the data. Valid choices are:nugget, exponential, gaussian, periodic, linear. [default: exponential]
-p, --print_model
Print in the title of the plot the function of the fit. [default: False]

Output:

The resulting output file consists of a pdf image containing the plot between the two distances matrices and the fitted model

Fitting:

For this script, the user supplies two distance matrices (i.e. resulting file from beta_diversity.py), along with the output filename (e.g. semivariogram), and the model to fit, as follows:

plot_semivariogram.py -x distance.txt -y unifrac.txt -o semivariogram_exponential.png

Modify the the default method to gaussian

plot_semivariogram.py -x distance.txt -y unifrac.txt -m gaussian -o semivariogram_gaussian.png

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