October 12, 2022

Updated code to make figures more easily accessible in the RMarkdown (HTML) file. Also, made all p-values exact per reviewer's comments
DFI-Bioinformatics · Oct 12, 2022 · 64eb9a3 · 64eb9a3
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Showing 36 changed files with 79,898 additions and 62,523 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/Data/SARS-CoV-2_Modeling.RData b/Data/SARS-CoV-2_Modeling.RData
diff --git a/Results/Figure_1.ai b/Results/Figure_1.ai
diff --git a/Results/Figure_1.pdf b/Results/Figure_1.pdf
diff --git a/Results/Figure_1_AI.pdf b/Results/Figure_1_AI.pdf
diff --git a/Results/Figure_2.ai b/Results/Figure_2.ai
diff --git a/Results/Figure_2_AI.pdf b/Results/Figure_2_AI.pdf
diff --git a/Results/Figure_3.pdf b/Results/Figure_3.pdf
diff --git a/Results/Figure_4.pdf b/Results/Figure_4.pdf
diff --git a/Results/Figure_4B.pdf b/Results/Figure_4B.pdf
diff --git a/Results/Figure_5.pdf b/Results/Figure_5.pdf
diff --git a/Results/Figure_S2.pdf b/Results/Figure_S2.pdf
diff --git a/Results/Figure_S3.pdf b/Results/Figure_S3.pdf
diff --git a/Results/Table_2.csv b/Results/Table_2.csv
@@ -16,3 +16,4 @@
 "desaminotyrosine (median [IQR])","28.10 [22.74, 46.94]","22.63 [21.00, 32.30]"," 0.028","nonnorm"
 "proteo_doms = 2 (%)","    9 (23.1) ","   16 (50.0) "," 0.035",""
 "entero_doms = 2 (%)","    3 ( 7.7) ","    3 ( 9.4) "," 1.000",""
+"mmp_score (median [IQR])"," 1.00 [0.00, 2.00]"," 2.00 [1.00, 4.00]","<0.001","nonnorm"
diff --git a/Results/Table_2_padjust.csv b/Results/Table_2_padjust.csv
@@ -1,18 +1,19 @@
 "","test","X","X0","X1","p","p.adj"
-"1","","n","   39","   32",NA,NA
-"2","nonnorm","InvSimpson (median [IQR])","10.77 [7.53, 18.05]","10.80 [5.74, 20.70]",0.931,0.931
-"3","nonnorm","lithocholic acid (median [IQR])","61.61 [4.30, 252.61]"," 9.76 [0.24, 60.07]",0.008,0.056
-"4","nonnorm","deoxycholic acid (median [IQR])","74.09 [18.61, 246.34]","10.68 [0.49, 62.50]",0.003,0.042
-"5","nonnorm","isodeoxycholic acid (median [IQR])"," 7.60 [0.70, 25.09]"," 2.89 [0.06, 10.93]",0.038,0.133
-"6","nonnorm","cholic acid (median [IQR])","16.21 [1.48, 215.59]"," 7.92 [0.79, 88.15]",0.214,0.3745
-"7","nonnorm","glycocholic acid (median [IQR])"," 0.43 [0.18, 2.83]"," 0.45 [0.03, 11.78]",0.511,0.550307692307692
-"8","nonnorm","3-oxolithocholic acid (median [IQR])"," 4.71 [0.64, 54.90]"," 1.88 [0.06, 14.03]",0.086,0.2408
-"9","nonnorm","alloisolithocholic acid (median [IQR])"," 0.44 [0.00, 2.79]"," 0.20 [0.00, 6.18]",0.482,0.550307692307692
-"10","nonnorm","taurocholic acid (median [IQR])"," 0.55 [0.22, 2.23]"," 0.30 [0.08, 24.06]",0.391,0.5474
-"11","nonnorm","butyrate (median [IQR])"," 0.51 [0.20, 2.39]"," 0.29 [0.06, 0.97]",0.286,0.444888888888889
-"12","nonnorm","propionate (median [IQR])"," 1.55 [0.47, 4.94]"," 0.75 [0.19, 1.62]",0.169,0.35
-"13","nonnorm","acetate (median [IQR])"," 3.87 [2.29, 20.44]"," 3.13 [1.17, 11.23]",0.175,0.35
-"14","nonnorm","succinate (median [IQR])"," 0.59 [0.26, 1.58]"," 0.50 [0.18, 1.38]",0.431,0.548545454545455
-"15","nonnorm","desaminotyrosine (median [IQR])","28.10 [22.74, 46.94]","22.63 [21.00, 32.30]",0.028,0.130666666666667
-"16","x2","proteo_doms = 2 (%)","    9 (23.1) ","   16 (50.0) ",0.035,0.07
-"17","x2","entero_doms = 2 (%)","    3 ( 7.7) ","    3 ( 9.4) ",1,1
+"1","nonnorm","InvSimpson (median [IQR])","10.77 [7.53, 18.05]","10.80 [5.74, 20.70]"," 0.931",0.931
+"2","nonnorm","lithocholic acid (median [IQR])","61.61 [4.30, 252.61]"," 9.76 [0.24, 60.07]"," 0.008",0.056
+"3","nonnorm","deoxycholic acid (median [IQR])","74.09 [18.61, 246.34]","10.68 [0.49, 62.50]"," 0.003",0.042
+"4","nonnorm","isodeoxycholic acid (median [IQR])"," 7.60 [0.70, 25.09]"," 2.89 [0.06, 10.93]"," 0.038",0.133
+"5","nonnorm","cholic acid (median [IQR])","16.21 [1.48, 215.59]"," 7.92 [0.79, 88.15]"," 0.214",0.3745
+"6","nonnorm","glycocholic acid (median [IQR])"," 0.43 [0.18, 2.83]"," 0.45 [0.03, 11.78]"," 0.511",0.550307692307692
+"7","nonnorm","3-oxolithocholic acid (median [IQR])"," 4.71 [0.64, 54.90]"," 1.88 [0.06, 14.03]"," 0.086",0.2408
+"8","nonnorm","alloisolithocholic acid (median [IQR])"," 0.44 [0.00, 2.79]"," 0.20 [0.00, 6.18]"," 0.482",0.550307692307692
+"9","nonnorm","taurocholic acid (median [IQR])"," 0.55 [0.22, 2.23]"," 0.30 [0.08, 24.06]"," 0.391",0.5474
+"10","nonnorm","butyrate (median [IQR])"," 0.51 [0.20, 2.39]"," 0.29 [0.06, 0.97]"," 0.286",0.444888888888889
+"11","nonnorm","propionate (median [IQR])"," 1.55 [0.47, 4.94]"," 0.75 [0.19, 1.62]"," 0.169",0.35
+"12","nonnorm","acetate (median [IQR])"," 3.87 [2.29, 20.44]"," 3.13 [1.17, 11.23]"," 0.175",0.35
+"13","nonnorm","succinate (median [IQR])"," 0.59 [0.26, 1.58]"," 0.50 [0.18, 1.38]"," 0.431",0.548545454545455
+"14","nonnorm","desaminotyrosine (median [IQR])","28.10 [22.74, 46.94]","22.63 [21.00, 32.30]"," 0.028",0.130666666666667
+"15","nonnorm","mmp_score (median [IQR])"," 1.00 [0.00, 2.00]"," 2.00 [1.00, 4.00]","<0.001",NA
+"16","x2","n","   39","   32","",NA
+"17","x2","proteo_doms = 2 (%)","    9 (23.1) ","   16 (50.0) "," 0.035",0.07
+"18","x2","entero_doms = 2 (%)","    3 ( 7.7) ","    3 ( 9.4) "," 1.000",1
diff --git a/Results/Table_4.png b/Results/Table_4.png
diff --git a/Results/Table_5.png b/Results/Table_5.png
diff --git a/Results/adjusted_heatmap.pdf b/Results/adjusted_heatmap.pdf
diff --git a/Results/bacteriocin_heatmap_total.pdf b/Results/bacteriocin_heatmap_total.pdf
diff --git a/Results/bacteriocins_toxins_card_heatmap.pdf b/Results/bacteriocins_toxins_card_heatmap.pdf
diff --git a/Results/card_heatmap_family.pdf b/Results/card_heatmap_family.pdf
diff --git a/Results/card_heatmap_total.pdf b/Results/card_heatmap_total.pdf
diff --git a/Results/covid_quant_metab_vital.pdf b/Results/covid_quant_metab_vital.pdf
diff --git a/Results/operon.pdf b/Results/operon.pdf
diff --git a/Results/shotgun_otu_lefse_analysis.pdf b/Results/shotgun_otu_lefse_analysis.pdf
diff --git a/Results/shotgun_pirate_alpha_diversity_evenness_vital.pdf b/Results/shotgun_pirate_alpha_diversity_evenness_vital.pdf
diff --git a/Results/shotgun_pirate_alpha_diversity_invsim_vital.pdf b/Results/shotgun_pirate_alpha_diversity_invsim_vital.pdf
diff --git a/Results/shotgun_pirate_alpha_diversity_richness_vital.pdf b/Results/shotgun_pirate_alpha_diversity_richness_vital.pdf
diff --git a/Results/shotgun_pirate_alpha_diversity_shannon_vital.pdf b/Results/shotgun_pirate_alpha_diversity_shannon_vital.pdf
diff --git a/Results/shotgun_relative_abundance.pdf b/Results/shotgun_relative_abundance.pdf
diff --git a/Results/shotgun_umap_umap_doms_vital.pdf b/Results/shotgun_umap_umap_doms_vital.pdf
diff --git a/Results/toxins_heatmap.pdf b/Results/toxins_heatmap.pdf
diff --git a/Results/unadjusted_heatmap.pdf b/Results/unadjusted_heatmap.pdf
diff --git a/Results/volcano_plot_total.pdf b/Results/volcano_plot_total.pdf