counting unique species in R

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1

yes, i want to do it in R so in order to do use those codes, i have to download the taxonomy.qza?

2

I tried and i got this error:

Warning messages:
1: In .local(object) : Coercing from data.frame class to character matrix
prior to building taxonomyTable.
This could introduce artifacts.
Check your taxonomyTable, or coerce to matrix manually.
2: In .local(object) : Coercing from data.frame class to character matrix
prior to building taxonomyTable.
This could introduce artifacts.
Check your taxonomyTable, or coerce to matrix manually.
3: In .local(object) : Coercing from data.frame class to character matrix
prior to building taxonomyTable.
This could introduce artifacts.
Check your taxonomyTable, or coerce to matrix manually.

3

Did you get this error when trying to make a phyloseq object in R? Can you post the codes you used?

4

ps <- taxonomy #is my taxonomic table

tax_table(ps) %>%
as("matrix") %>%
as_tibble(rownames = "Taxon") %>%
gather("Rank", "Name", rank_names(ps)) %>%
na.omit() %>% # remove rows with NA value
group_by(Rank) %>%
summarize(ntaxa = length(unique(Name))) %>%
mutate(Rank = factor(Rank, rank_names(ps))) %>%
arrange(Rank)

5

You need to make a phyloseq object first and then run the R codes you used.

Below is an example based on the metadata, feature table, taxonomy file and rooted-tree from the "Moving Pictures" tutorial.

library(tidyverse) 
library(qiime2R) 
library(phyloseq) 

# Make a phyloseq object in R
metadata <- read_tsv("metadata.tsv", comment = "#q2:type") 

table <- read_qza("table.qza")
count_tab <- table$data %>% as.data.frame() 

taxonomy <- read_qza("taxonomy.qza")
tax_tab <- taxonomy$data %>% 
  as.data.frame() %>%
  separate(Taxon, sep = ";", c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")) %>% 
  column_to_rownames("Feature.ID") %>%
  select(-Confidence)

tree <- read_qza("rooted-tree.qza")

ps <- phyloseq(otu_table(as.matrix(count_tab), taxa_are_rows = T),
               phy_tree(tree$data), 
               tax_table(as.matrix(tax_tab)), 
               sample_data(metadata %>% column_to_rownames("sample-id")))

# Compute number of taxa
tax_table(ps) %>%
  as("matrix") %>%
  as_tibble(rownames = "OTU") %>%
  gather("Rank", "Name", rank_names(ps)) %>%
  na.omit() %>% # remove rows with NA value
  group_by(Rank) %>%
  summarize(ntaxa = length(unique(Name))) %>% # compute number of unique taxa
  mutate(Rank = factor(Rank, rank_names(ps))) %>%
  arrange(Rank)

# A tibble: 7 x 2
  Rank    ntaxa
  <fct>   <int>
1 Kingdom     3
2 Phylum     19
3 Class      38
4 Order      60
5 Family    109
6 Genus     198
7 Species   105

-Yanxian

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