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################## INSTRUCTIONS ##################

This set of snippets is provided as supporting
material to the article:

	Clonal analysis of the neonatal mouse heart 
	using nearest neighbor modeling. 
	(Bakovic et al, 2020)

Refer to the article for more details about the
methods.

The directory is organized as follows:
+
	-README.txt
	/scripts/
	/data/
	+example_results/
		/scripts/
		/data/
		/Rdata/
		/plots/
		/model_files/

Requirements:
- R (>3.5)
- Python (>2.7)
- Python packages:
	- numpy
	- pandas

To execute the snippets, open the terminal, go to
the scripts/ directory and run the scripts as shown:

Snippet 1:
python snippet_6_1.py <ImageJ_results_directory>

Snippet 2:
Rscript snippet_6_2.R

Snippet 3:
Rscript snippet_6_3.R

Snippet 4:
Rscript snippet_6_4.R

Snippet 5:
Rscript snippet_6_5.R

Snippet 6:
Rscript snippet_6_6.R

Snippet 7:
Rscript snippet_6_7.R

The results are printed either on the screen or
published as plots in the plots/ directory. Refer
to each snippet to change parameters as required
by the dataset being used.

The example_results/ directory shows the expected
directory structure after a successful execution.

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