A bunch of poorly-written ad-hoc python scripts to generate the alluvial diagram appears in my ISME Publication:
The scripts here explain only the generation of the alluvial diagram. To get a similar result for your dataset, first you need to analyze the same FASTA file with multiple different damarcation methods (such as assigning taxonomy to reads, OTU clustering, MED analysis, etc). Then you need to open each script and edit paths for input files (I wasn't kidding or being modest when I said "poorly-written"). When you run them in the correct order, you should get an output from the last one similar to this:
taxa,otu,med,size
Streptococcus,3349,000005591,557045
Streptococcus,3349,000004955,554047
Veillonella,3481,000003105,356556
Streptococcus,962,000005530,239505
Neisseria,1844,000003465,198265
Fusobacterium,3540,000003684,166689
Porphyromonas,3716,000005301,157760
Prevotella,2433,000001012,145605
Streptococcus,497,000005526,1035
Streptococcus,962,000005526,126854
Gemella,1975,000004822,111216
Actinomyces,1003,000002612,104190
Granulicatella,3226,000002347,100576
Corynebacterium,2654,000005031,94972
Pasteurella,612,000003262,81356
Pasteurella,612,000003227,73804
Fusobacterium,501,000003637,7728
Fusobacterium,3540,000003637,60484
Streptococcus,3223,000005538,1599
Streptococcus,1846,000005538,6589
Streptococcus,2604,000005538,1667
Streptococcus,3349,000005538,57257
Leptotrichia,487,000004781,58892
Neisseria,4182,000003433,7029
Neisseria,1844,000003433,50301
Pasteurella,612,000005182,55451
Actinobacillus,796,000003361,6565
Actinobacillus,612,000003361,45592
Fusobacterium,2889,000003638,4264
Fusobacterium,3540,000003638,44902
Actinomyces,1354,000002895,42699
Prevotella,3964,000004447,42279
Rothia,2389,000002864,40165
Prevotella,2433,000004419,38738
Capnocytophaga,2928,000002397,38377
Campylobacter,998,000000313,38028
Pasteurella,612,000005177,37281
Actinobacillus,796,000003360,3727
Actinobacillus,612,000003360,31324
Pasteurella,612,000003263,34367
Pasteurella,612,000003225,32745
Collimonas,4148,000003532,32196
Syntrophococcus,4229,000000346,30981
Corynebacterium,2124,000002608,30579
Prevotella,2433,000005422,28308
Oribacterium,80,000004614,28272
Selenomonas,3974,000005135,26897
Bacteroides,2546,000004009,26729
Veillonella,1215,000005139,4555
Veillonella,3481,000005139,21818
Actinobacillus,612,000003356,25568
Porphyromonas,3716,000003840,25476
Actinobacillus,796,000003366,2149
Actinobacillus,612,000003366,23294
Fusobacterium,2889,000003647,2904
Fusobacterium,3540,000003647,22164
Prevotella,2273,000004268,24634
Leptotrichia,1750,000004735,24620
Capnocytophaga,621,000004855,24385
Rothia,2389,000002865,24216
Prevotella,2427,000004476,21082
Neisseria,4182,000003434,2293
Neisseria,1844,000003434,17746
Bacteroides,2546,000004010,18205
Fusobacterium,2889,000003636,2033
Fusobacterium,3540,000003636,15856
Veillonella,1522,000005168,2545
Veillonella,3481,000005168,14486
Atopobium,3539,000002926,17575
Johnsonella,2617,000003717,17151
Fusobacterium,3540,000003665,16168
Neisseria,1844,000003564,14615
Neisseria,3085,000003564,1058
Prevotella,2433,000001013,15706
Bacteroides,2546,000003829,13187
Bacteroides,2417,000003829,1824
Actinobacillus,796,000003365,2461
Actinobacillus,612,000003365,12265
Porphyromonas,3716,000003842,14764
Capnocytophaga,673,000001531,1823
Capnocytophaga,621,000001531,12945
Streptococcus,3349,000005557,2059
Streptococcus,1846,000005557,1241
Streptococcus,962,000005557,10194
Bacteroides,2546,000003837,14283
Parvimonas,3401,000000923,13871
Actinomyces,4445,000005035,13661
Parasegetibacter,441,000003963,13441
Bacteroides,2546,000003984,11262
Bacteroides,2417,000003984,1373
Leptotrichia,487,000002031,13082
Prevotella,2433,000004417,12803
Moryella,3131,000001488,12573
Actinobacillus,612,000005225,11598
Selenomonas,3974,000003177,12135
Prevotella,2469,000000443,12064
Selenomonas,3974,000003178,11391
Prevotella,3964,000005428,11158
Johnsonella,2617,000003710,11113
Actinomyces,4445,000005034,11056
Prevotella,2433,000004416,10664
Leptotrichia,4429,000005474,10657
Porphyromonas,3716,000003841,10092
Catonella,795,000005492,10357
Bacteroides,2417,000003830,1100
Bacteroides,2546,000003830,8977
Neisseria,1844,000003470,10033
Moryella,3131,000001486,9796
Porphyromonas,3716,000005300,9687
Prevotella,16,000001696,9518
Fusobacterium,3540,000003651,8975
Pasteurella,612,000003230,9280
Rothia,2389,000002866,9251
Streptococcus,962,000005556,8669
Actinobacillus,612,000005215,7793
Actinobacillus,612,000005221,6534
Actinobacillus,796,000005221,2016
Collimonas,4148,000003533,8422
Campylobacter,4367,000000314,8223
Leptotrichia,487,000004720,6619
Leptotrichia,1689,000004720,1123
Leptotrichia,3402,000004689,8170
Prevotella,2655,000004362,8109
Actinobaculum,4113,000002616,8046
Tannerella,1159,000003976,7910
Then you can go to http://raw.densitydesign.org, paste this output into the input box on the web site, select 'alluvial diagram', set you width and height (to something like 900 x 2000), and finally set "sorty by" option to "automatic".
Which should give you something like this:
I apologize for the sloppy code. Regenerating figures in a publication should be much more straightforward. This was a last minute figure, and my eager to get it done empowered my desire to do the right thing. I am hoping to come back to this at some point to give the code a facelift. Meanwhile please don't hesitate to send me your questions: meren at mbl edu.