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/home/yonatanf/alm_lib/mipython.sh

Now, I do what you need to. I usually start by following some of the commands in his demo by looking at the commands and typing them in with my files and my specifics:

more /home/yonatanf/alm_lib/survey/demo/run_demo.py

This stuff below I need to do. This specifically makes an ordered heatmap of Mystic Lake depths:

Wiki MarkupIn \ [1\]: file = 'eOTU_parallel/ML_Q_unique_final.mat.lin'

Wiki MarkupIn \ [2\]: counts, lins = SM.fromTxt(file, lin=True)

Wiki MarkupIn \ [3\]: counts = counts.remove_rows(\['MSB','MEB','M3.2','M8.2','M22'\])

Wiki MarkupIn \ [4\]: fracs = counts.normalize()

Wiki MarkupIn \ [5\]: D = fracs.dist_mat(axis='rows', metric='JSsqrt')

Wiki MarkupIn \ [6\]: order = \ ['M21', 'M20', 'M19', 'M17', 'M16', 'M15', 'M14', 'M13', 'M12', 'M11', 'M10', 'M9', 'M8', 'M7', 'M6', 'M5', 'M4', 'M3.1', 'M1.5', 'M0'\]

Wiki MarkupIn \ [7\]: Dorder = D.reindex(index=order, columns=order)unmigrated-wiki-markup

In \ [8\]: Dorder.plot_dist_heatmap(sort_rows=False, sort_cols=False, plot_row_labels=True, row_label_width = 0.06)

If you encounter problems, post them to his issues page:

https://bitbucket.org/yonatanf/survey/issues