ASV data

Below we will use the provided ASV data to combine two data frames and perform some typical calculations.

1 Compile ASV and metadata

library(tidyverse)

Warning: package 'ggplot2' was built under R version 4.2.3

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Warning: package 'readr' was built under R version 4.2.3

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# head(metadata)
asv_long <- asv_table %>%
  pivot_longer(starts_with("Gorda"), names_to = "SAMPLEID") %>% 
  left_join(metadata %>% select(SAMPLEID = SAMPLE, everything()))

Joining with `by = join_by(SAMPLEID)`

# View(asv_long)

2 Get temperature data from data frame

Isolate samples that have a temperature greater than 15 C.

asv_long %>% 
  filter(temp > 15)

# A tibble: 42,039 × 10
   FeatureID Taxon SAMPLEID value VENT  SITE  Sample_or_Control SAMPLETYPE DEPTH
   <chr>     <chr> <chr>    <int> <chr> <chr> <chr>             <chr>      <chr>
 1 00056209… Euka… GordaRi…     0 Cand… Gord… Sample            Vent       2730 
 2 00056209… Euka… GordaRi…     0 Sir … Gord… Sample            Vent       2732 
 3 00056209… Euka… GordaRi…     0 Cand… Gord… Sample            Vent       2730 
 4 00056209… Euka… GordaRi…     0 Sir … Gord… Sample            Vent       2732 
 5 00056209… Euka… GordaRi…     0 Mt E… Gord… Sample            Vent       2707 
 6 00056209… Euka… GordaRi…     0 Mt E… Gord… Sample            Vent       2707 
 7 00056209… Euka… GordaRi…     0 Sir … Gord… Sample            Vent       2732 
 8 00056209… Euka… GordaRi…     0 Mt E… Gord… Sample            Vent       2707 
 9 00056209… Euka… GordaRi…     0 Cand… Gord… Sample            Vent       2730 
10 00096455… Euka… GordaRi…     0 Cand… Gord… Sample            Vent       2730 
# ℹ 42,029 more rows
# ℹ 1 more variable: temp <dbl>

# Make a list of vent sites from Gorda Ridge that had a temperature greater than 15 C.

What are the average temperatures at the vent, plume, versus background samples? And how many of each sample are there?

asv_long %>% 

3 Parse taxon names

asv_long %>% 

4 Calculate relative abundance

Create a table with sequence counts and ASV counts by supergroup.

asv_long %>% 

4.1 Make a bar plot

asv_long %>%