Import and subset data

## Warning in amp_load(otutable = otutable, metadata = metadata): Only 44 of 63 unique sample names match between metadata and otutable. The following unmatched samples have been removed:
## otutable (19): 
##  "MQ180819-127", "MQ180801-199", "MQ171129-261", "MQ180819-149", "MQ180819-14", "MQ180309-33", "MQ180801-219", "MQ180819-128", "MQ180819-146", "MQ180819-148", "MQ180323-30", "MQ180525-70", "MQ180819-150", "MQ180819-145", "MQ180819-16", "MQ180819-147", "MQ180819-123", "MQ180819-124", "MQ180819-151"

Rarefraction curves

Quality Check

Read abundance

These can be used to compare the diversity between samples. I.e. how many OTUs constitute 75% of all reads in the sample.

## Scale for 'x' is already present. Adding another scale for 'x', which
## will replace the existing scale.

Core plots

##        OTU Abundance         Phylum                       Genus
## 1    OTU_4     11.22    Nitrospirae                  Nitrospira
## 2    OTU_7      3.82    Nitrospirae                  Nitrospira
## 3    OTU_6      3.00 Proteobacteria              Hyphomicrobium
## 4    OTU_5      2.92 Proteobacteria                        MNG7
## 5    OTU_8      2.81 Proteobacteria    f__Gallionellaceae_OTU_8
## 6   OTU_33      1.75 Proteobacteria                  Woodsholea
## 7   OTU_16      1.58 Proteobacteria             f__A0839_OTU_16
## 8  OTU_591      1.02    Nitrospirae                  Nitrospira
## 9   OTU_36      0.98  Acidobacteria                     Btb7_22
## 10  OTU_18      0.90  Acidobacteria               Blastocatella
## 11  OTU_66      0.71 Proteobacteria                 Gallionella
## 12  OTU_26      0.59 Proteobacteria f__Xanthobacteraceae_OTU_26
## 13  OTU_87      0.52 Proteobacteria              Hyphomicrobium

Heatmaps Phylum by Waterworks

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Heatmaps Phylum by Depth

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Heatmaps Genera by Waterworks

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Heatmaps Genera by Depth

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Heatmaps Genera by Waterworks and Depth

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Heatmaps genera with known MnOBs by Depth

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Boxplots genera with known MnOBs by Waterworks

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PCAs

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CCAs variation explained by waterworks

Venn

## 10 samples and 39 OTUs have been filtered 
## Before: 44 samples and 1411 OTUs
## After: 34 samples and 1372 OTUs