WP1 DNAsense data
Ines L Breda
May 5, 2017
knitr::opts_chunk$set(echo=FALSE, message = FALSE, warning = FALSE, results= FALSE)Load package
Loading all code needed.
Importing data
Import metafile from DNAsense.
Merging into ampvis format
The three files are converted into a simple list that can be read by all ampvis2 functions. Here we store the list in the object d.
Data quality
Alpha diversity
Rarefaction curves
Data overview
Heatmaps
Phylum
Genus
Top25 most abundant genera
Genera with knon MnOB
Boxplots
MnOB in Source water and Filter media
MnOB in Filter media
Functional information
Identification of MnOBs in top25 genera
Statistical analysis
Ordination
PCA Source water and Filter material
PCA Filter material
PCA Filter material without Polystyrene
Testing significance of groupings (PCA)
Demonstration for PCA 1 (incl. Source water and Filter materials)
##
## ***FACTORS:
##
## Centroids:
## PC1 PC2
## MaterialCalcium Carbonate -0.1984 -0.5151
## MaterialManganese Oxide -0.2279 0.1588
## MaterialMatured Quartz -0.1992 0.5681
## MaterialPolystyrene 0.8906 -0.0644
## MaterialSource Water -0.0257 0.4586
## MaterialVirgin Quartz -0.2480 -0.4531
##
## Goodness of fit:
## r2 Pr(>r)
## Material 0.9849 0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
Differential abundance
## $DESeq2_results
## log2 fold change (MLE): Material Virgin.Quartz vs Calcium.Carbonate
## Wald test p-value: Material Virgin.Quartz vs Calcium.Carbonate
## DataFrame with 682 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## OTU_1 2.728942e+03 1.021696 0.9969945 1.0247760 0.30546891
## OTU_10 6.692060e+02 1.087190 0.7033783 1.5456690 0.12218452
## OTU_100 3.296737e+01 1.448934 1.6142194 0.8976068 0.36939523
## OTU_1000 1.192554e+00 5.068672 2.8682217 1.7671828 0.07719762
## OTU_1001 3.605871e-02 1.467226 4.8566061 0.3021093 0.76256871
## ... ... ... ... ... ...
## OTU_991 0.6235414 4.4507193 4.737960 0.9393746 0.3475384
## OTU_992 0.1036858 3.0047602 4.782988 0.6282183 0.5298610
## OTU_993 0.7816003 0.5054118 4.856606 0.1040669 0.9171163
## OTU_995 2.0134823 1.4673229 2.604788 0.5633175 0.5732187
## OTU_996 0.2171610 2.0700506 4.841436 0.4275696 0.6689645
## padj
## <numeric>
## OTU_1 0.4665560
## OTU_10 0.2596421
## OTU_100 0.5271297
## OTU_1000 NA
## OTU_1001 NA
## ... ...
## OTU_991 NA
## OTU_992 NA
## OTU_993 NA
## OTU_995 0.7160656
## OTU_996 NA
##
## $plot_MA
##
## $DESeq2_results_significant
## baseMean log2FoldChange lfcSE stat pvalue padj
## 1 8.998219 -23.439098 3.465152 -6.764234 1.340160e-11 5.240025e-09
## 2 8.694753 -27.101774 4.193554 -6.462722 1.028358e-10 2.010441e-08
## 3 6.011038 -23.811962 3.806638 -6.255378 3.965545e-10 5.168427e-08
## 4 7.221037 -23.681886 4.216683 -5.616236 1.951619e-08 1.907707e-06
## 5 37.950451 -25.350656 4.711771 -5.380282 7.436928e-08 5.815678e-06
## 6 8.895957 8.546689 1.618198 5.281610 1.280533e-07 8.344804e-06
## 7 11.620608 -23.664449 4.712094 -5.022066 5.111857e-07 2.260269e-05
## 8 216.608019 7.540985 1.508679 4.998402 5.780740e-07 2.260269e-05
## 9 16.322761 -23.642586 4.711960 -5.017570 5.232922e-07 2.260269e-05
## 10 15.424261 -23.697167 4.711979 -5.029133 4.927032e-07 2.260269e-05
## 11 10.512457 -23.180524 4.689959 -4.942586 7.709321e-07 2.740313e-05
## 12 10.636657 8.256356 1.703070 4.847926 1.247591e-06 4.065067e-05
## 13 5.872168 -22.428333 4.712553 -4.759275 1.942900e-06 5.843647e-05
## 14 192.315818 -5.126326 1.089015 -4.707304 2.510140e-06 7.010461e-05
## 15 57.188837 7.438462 1.637572 4.542373 5.562452e-06 1.449946e-04
## 16 822.854729 6.759287 1.590024 4.251061 2.127604e-05 5.199333e-04
## 17 139.839428 6.906684 1.630584 4.235712 2.278291e-05 5.240070e-04
## 18 18.795400 -5.368319 1.279028 -4.197187 2.702509e-05 5.870451e-04
## 19 12.363858 7.265816 1.777343 4.088022 4.350675e-05 8.953230e-04
## 20 123.199790 -5.720083 1.412874 -4.048544 5.153729e-05 1.007554e-03
## 21 23.509631 6.773325 1.691079 4.005327 6.193176e-05 1.153110e-03
## 22 36.998001 6.647273 1.728794 3.845034 1.205356e-04 2.142246e-03
## 23 27.509026 5.367353 1.505339 3.565544 3.631028e-04 6.150819e-03
## 24 29.797932 6.106258 1.717507 3.555303 3.775439e-04 6.150819e-03
## 25 9.954150 6.888203 1.981145 3.476880 5.072846e-04 7.933931e-03
## 26 24.366374 6.027097 1.749571 3.444899 5.712723e-04 8.272869e-03
## 27 3.643501 6.366170 1.843450 3.453400 5.535677e-04 8.272869e-03
## 28 145.357220 5.799655 1.699581 3.412403 6.439293e-04 8.992013e-03
## 29 14.767601 6.003918 1.766876 3.398042 6.786993e-04 9.150740e-03
## 30 16.966197 -8.851474 2.613567 -3.386741 7.072810e-04 9.218229e-03
## 31 84.698253 6.261060 1.857172 3.371286 7.481808e-04 9.436732e-03
## Tax
## 1 OTU_57
## 2 OTU_46
## 3 OTU_178
## 4 OTU_138
## 5 OTU_35
## 6 OTU_72
## 7 OTU_115
## 8 OTU_43
## 9 OTU_69
## 10 OTU_85
## 11 OTU_112
## 12 OTU_114
## 13 OTU_147
## 14 OTU_7
## 15 OTU_150
## 16 OTU_26
## 17 OTU_62
## 18 OTU_58
## 19 OTU_166
## 20 OTU_16
## 21 OTU_116
## 22 OTU_130
## 23 OTU_142
## 24 OTU_196
## 25 OTU_238
## 26 OTU_189
## 27 OTU_34
## 28 OTU_47
## 29 OTU_651
## 30 OTU_37
## 31 OTU_214
##
## $plot_sig
##
## $sig_res_plot_data
## Source: local data frame [465 x 12]
## Groups: Sample [15]
##
## # A tibble: 465 x 12
## Sample Tax Count Abundance baseMean log2FoldChange lfcSE
## <chr> <fctr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 16SAMP-13400 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 2 16SAMP-13401 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 3 16SAMP-13402 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 4 16SAMP-13403 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 5 16SAMP-13404 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 6 16SAMP-13405 OTU_57 271 0.665602358 8.998219 -23.4391 3.465152
## 7 16SAMP-13406 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 8 16SAMP-13407 OTU_57 6 0.014013126 8.998219 -23.4391 3.465152
## 9 16SAMP-13408 OTU_57 0 0.000000000 8.998219 -23.4391 3.465152
## 10 16SAMP-13409 OTU_57 1 0.002960682 8.998219 -23.4391 3.465152
## # ... with 455 more rows, and 5 more variables: stat <dbl>, pvalue <dbl>,
## # padj <dbl>, Significant <chr>, Material <fctr>
##
## $Clean_results
## Source: local data frame [682 x 8]
## Groups: Taxonomy, padj [682]
##
## # A tibble: 682 x 8
## Taxonomy padj Log2FC `Calcium Carbonate` `Manganese Oxide`
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 OTU_57 5.2e-09 -23.0 0.222 0.005
## 2 OTU_46 2.0e-08 -27.0 0.235 0.002
## 3 OTU_178 5.2e-08 -24.0 0.160 0.001
## 4 OTU_138 1.9e-06 -24.0 0.196 0.001
## 5 OTU_35 5.8e-06 -25.0 0.957 0.002
## 6 OTU_72 8.3e-06 8.5 0.000 0.028
## 7 OTU_115 2.3e-05 -24.0 0.318 0.000
## 8 OTU_43 2.3e-05 7.5 0.000 0.031
## 9 OTU_69 2.3e-05 -24.0 0.446 0.000
## 10 OTU_85 2.3e-05 -24.0 0.422 0.000
## # ... with 672 more rows, and 3 more variables: `Matured Quartz` <dbl>,
## # Polystyrene <dbl>, `Virgin Quartz` <dbl>
| Taxonomy | padj | Log2FC | Calcium Carbonate | Manganese Oxide | Matured Quartz | Polystyrene | Virgin Quartz |
|---|---|---|---|---|---|---|---|
| OTU_57 | 0.0e+00 | -23.0 | 0.222 | 0.005 | 0.000 | 0.002 | 0.000 |
| OTU_46 | 0.0e+00 | -27.0 | 0.235 | 0.002 | 0.000 | 0.000 | 0.000 |
| OTU_178 | 1.0e-07 | -24.0 | 0.160 | 0.001 | 0.001 | 0.000 | 0.000 |
| OTU_138 | 1.9e-06 | -24.0 | 0.196 | 0.001 | 0.000 | 0.000 | 0.000 |
| OTU_35 | 5.8e-06 | -25.0 | 0.957 | 0.002 | 0.000 | 0.001 | 0.000 |
| OTU_72 | 8.3e-06 | 8.5 | 0.000 | 0.028 | 0.017 | 0.001 | 0.133 |
| OTU_115 | 2.3e-05 | -24.0 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| OTU_43 | 2.3e-05 | 7.5 | 0.000 | 0.031 | 1.008 | 0.227 | 0.069 |
| OTU_69 | 2.3e-05 | -24.0 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| OTU_85 | 2.3e-05 | -24.0 | 0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
Core community analysis
Venn diagrams
Rankabundance
Frequency plots
Core plots
## Display Frequency freq_A Abundance
## 1 OTU_1 15 12 12.47
## 2 OTU_3 14 11 10.21
## 3 OTU_4 15 15 7.11
## 4 OTU_5 14 11 4.18
## 5 OTU_13 15 12 3.90
## 6 OTU_10 14 12 3.19
## 7 OTU_11 15 13 2.51
## 8 OTU_9 15 12 2.20
## 9 OTU_8 15 13 1.72
## 10 OTU_12 12 11 1.45
## 11 OTU_18 14 14 1.45
## 12 OTU_29 15 13 1.28
## 13 OTU_17 15 15 1.07
## 14 OTU_28 12 11 1.02
## 15 OTU_15 15 15 0.83
## 16 OTU_21 12 12 0.66
## 17 OTU_27 14 14 0.61
## 18 OTU_31 15 13 0.45
## 19 OTU_40 15 11 0.39