overhaul examples

solislemuslab · Jan 17, 2024 · c4fbde9 · c4fbde9
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diff --git a/example/README.md b/example/README.md
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+# Examples
+
+The purpose of this folder is to provide worked example of MiNAA's inputs, execution, and outputs.
+
+`g.csv` is the adjacency matrix for the network G.
+`h.csv` is the adjacency matrix for the network H.
+`bio.csv` is the biological similarity matrix .
+
+Once MiNAA is successfully compiled, the examples below can be run from this project's root directory. See the main README for compilation steps.
+
+## Example 1
+
+`./minaa.exe example/g.csv example/h.csv -a=0.6 -g`
+
+Output to: `g-h-a0.6/`
+
+Here we align network **g** with network **h** using no biological data. `-a=0.6` sets alpha equal to 0.6, meaning 60% of the topological cost function comes from similarity calculated by GDVs, and 40% from simpler node degree data.
+
+## Example 2
+
+`./minaa.exe example/g.csv example/h.csv -B=example/bio.csv -b=0.85 -st=0.5 -s`
+
+Output to: `g-h/`
+
+Here we align network **g** with network **h** using topological information and the given biological similarity matrix, **bio**. Since we've provided a similarity matrix instead of a cost matrix (the default), we have to flag that with `-s`. Since alpha was unspecified, it defaults to 1. Since beta was set to 0.85, 85% of the cost weight is from the calculated topological cost matrix, and 15% is from **bio**. Since the similarity threshold `-st=` was set to 0.5, any aligned pair with similarity score less than or equal to 0.5 is excluded from the alignment results.
+
+## Example 3
+
+`./minaa.exe example/g.csv example/h.csv -Galias=nonsmoker -Halias=smoker -p -t`
+
+Output to: `nonsmoker-smoker-2024_01_16-22_05_34/`
+
+Here we align network **g** with network **h**, where **g** is given the alias "nonsmoker", and **h** is given the alias "smoker". The timestamp option `-t` was specified, so the name of the output folder will be nonsmoker-smoker-T, where T is the date and time of execution. Additionally, because the passthrough option `-p` was specified, g.csv and h.csv will be passed through to the output folder as nonsmoker.csv and smoker.csv, respectively.
+
+## Attributions
+
+`g.csv`, `h.csv`, and `bio.csv` were produced using data from the paper cited below, which is available [here](https://github.com/lichen-lab/SICS/tree/master/data).
+
+```txt
+Xiao, Jian, et al. “A phylogeny-regularized sparse regression model for predictive modeling of Microbial Community Data.” 
+Frontiers in Microbiology, vol. 9, 19 Dec. 2018, https://doi.org/10.3389/fmicb.2018.03112. 
+```
diff --git a/example/bio.csv b/example/bio.csv
diff --git a/example/g-h-a0.6/alignment_list.csv b/example/g-h-a0.6/alignment_list.csv
@@ -0,0 +1,75 @@
+34.09,,
+"g70","h70",0.713643
+"g46","h155",0.6
+"g7","h161",0.6
+"g169","h125",0.6
+"g95","h153",0.6
+"g166","h18",0.6
+"g116","h169",0.6
+"g174","h137",0.6
+"g68","h142",0.6
+"g19","h25",0.6
+"g20","h128",0.6
+"g22","h160",0.6
+"g65","h7",0.6
+"g24","h162",0.6
+"g28","h87",0.6
+"g54","h123",0.6
+"g53","h63",0.6
+"g103","h117",0.6
+"g37","h110",0.6
+"g131","h51",0.593022
+"g142","h31",0.593022
+"g12","h124",0.589163
+"g73","h115",0.584753
+"g52","h127",0.582448
+"g42","h145",0.579945
+"g133","h32",0.576386
+"g120","h101",0.576386
+"g150","h22",0.576386
+"g106","h107",0.576386
+"g105","h132",0.576173
+"g112","h109",0.574572
+"g172","h44",0.569101
+"g119","h103",0.568454
+"g164","h60",0.567943
+"g92","h68",0.567943
+"g137","h174",0.566874
+"g123","h73",0.564988
+"g91","h55",0.562526
+"g63","h129",0.560852
+"g59","h152",0.559406
+"g157","h6",0.558591
+"g128","h173",0.558591
+"g32","h122",0.557958
+"g45","h156",0.555522
+"g1","h146",0.553349
+"g35","h135",0.549792
+"g43","h56",0.546033
+"g56","h118",0.540678
+"g154","h21",0.540678
+"g8","h138",0.539013
+"g30","h130",0.538856
+"g51","h104",0.536551
+"g6","h5",0.531083
+"g155","h120",0.530757
+"g139","h30",0.516315
+"g173","h106",0.516061
+"g167","h134",0.513479
+"g108","h28",0.508566
+"g130","h102",0.498883
+"g109","h93",0.495011
+"g90","h90",0.491157
+"g115","h72",0.490489
+"g16","h96",0.446617
+"g125","h157",0.44302
+"g14","h171",0.437641
+"g126","h121",0.398194
+"g17","h14",0.384953
+"g58","h13",0.382559
+"g23","h81",0.376354
+"g81","h23",0.375077
+"g74","h74",0.373053
+"g82","h71",0.35058
+"g13","h43",0.347457
+"g71","h17",0.346704
diff --git a/example/g-h-a0.6/alignment_matrix.csv b/example/g-h-a0.6/alignment_matrix.csv
diff --git a/example/g-h-a0.6/g_gdvs.csv b/example/g-h-a0.6/g_gdvs.csv
diff --git a/example/g-h-a0.6/h_gdvs.csv b/example/g-h-a0.6/h_gdvs.csv
diff --git a/example/g-h-a0.6/log.txt b/example/g-h-a0.6/log.txt
@@ -0,0 +1,19 @@
+Executing:   ./minaa.exe example/g.csv example/h.csv -a=0.6 -g 
+Y_M_D-H_M_S: 2024_01_16-22_02_40
+
+INPUTS
+G File:               g.csv
+H File:               h.csv
+Alpha:                0.600
+Beta:                 1.000
+Similarity threshold: 0.0000
+
+BEGINNING ALIGNMENT
+Reading graph files............................done. (9ms)
+Calculating GDVs...............................done. (19ms)
+Writing GDVs to files..........................done. (4ms)
+Calculating the topological cost matrix........done. (16ms)
+Writing the topological cost matrix to file....done. (5ms)
+Aligning the graphs............................done. (48ms)
+Writing the alignment to file..................done. (1ms)
+ALIGNMENT COMPLETED (106ms)
diff --git a/example/g-h-a0.6/topological_costs.csv b/example/g-h-a0.6/topological_costs.csv
diff --git a/example/g-h/alignment_list.csv b/example/g-h/alignment_list.csv
@@ -0,0 +1,75 @@
+10.0745,,
+"g103","h103",1
+"g142","h142",1
+"g22","h22",1
+"g169","h169",0.990114
+"g7","h7",0.984648
+"g116","h117",0.98001
+"g20","h21",0.972506
+"g166","h162",0.969195
+"g174","h174",0.96678
+"g28","h25",0.964088
+"g53","h51",0.961541
+"g37","h32",0.961388
+"g123","h123",0.958234
+"g106","h107",0.954588
+"g73","h73",0.954209
+"g95","h101",0.954116
+"g19","h18",0.95382
+"g68","h87",0.950494
+"g150","h153",0.949326
+"g131","h161",0.946096
+"g54","h110",0.937734
+"g46","h118",0.937734
+"g63","h63",0.932344
+"g12","h5",0.931352
+"g65","h31",0.929845
+"g24","h127",0.927314
+"g56","h55",0.926232
+"g137","h137",0.92356
+"g43","h44",0.923038
+"g133","h160",0.922529
+"g52","h115",0.922044
+"g51","h60",0.916516
+"g120","h125",0.912207
+"g35","h68",0.903871
+"g105","h132",0.90233
+"g112","h109",0.901711
+"g154","h155",0.89893
+"g119","h124",0.898653
+"g42","h56",0.89063
+"g173","h173",0.888986
+"g164","h135",0.884854
+"g128","h128",0.882942
+"g32","h129",0.878578
+"g157","h6",0.877423
+"g172","h145",0.877191
+"g59","h122",0.876526
+"g45","h156",0.873076
+"g30","h28",0.87189
+"g8","h30",0.869622
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+"g6","h152",0.863599
+"g1","h131",0.860218
+"g92","h104",0.851962
+"g155","h120",0.847566
+"g90","h90",0.845806
+"g108","h106",0.822251
+"g139","h138",0.82207
+"g167","h20",0.813515
+"g130","h130",0.795234
+"g109","h93",0.793114
+"g115","h116",0.781862
+"g16","h12",0.745638
+"g14","h171",0.687009
+"g125","h8",0.681904
+"g74","h74",0.678492
+"g17","h14",0.659007
+"g126","h43",0.644468
+"g23","h23",0.634079
+"g81","h17",0.623758
+"g71","h71",0.617906
+"g82","h82",0.607243
+"g13","h13",0.606327
+"g70","h70",0.594328
+"g58","h58",0.588709