Convert Phyloseq to AmpVis2 format in R

gistfile1.txt

```{r phyloseq-ampvis2}
library("ampvis2")

# Load data into ampvis
otu.table <- t(otu_table(ps1, taxa_are_rows = FALSE))
otu.table <- as.data.frame(otu.table)
otu.table <- rownames_to_column(otu.table, var = "OTU")
head(rownames(otu.table))
head(colnames(otu.table))
nrow(otu.table)

tax.table <- as.data.frame(tax_table(ps1))
tax.table <- rownames_to_column(tax.table, var = "OTU")
head(rownames(tax.table))
head(colnames(tax.table))
nrow(tax.table)

my_otu_table <- left_join(otu.table, tax.table, by = "OTU")
nrow(my_otu_table)
colnames(my_otu_table)
head(rownames(my_otu_table))

my_otu_table <- column_to_rownames(my_otu_table, var = "OTU")
head(rownames(my_otu_table))
colnames(my_otu_table)
nrow(my_otu_table)

my_metadata <- as.tibble(sample_data(ps1))
class(my_metadata)
head(rownames(my_metadata))
nrow(my_metadata)
ncol(my_metadata)

my_tree <- phy_tree(ps1)

ps1.av2 <- amp_load(otutable = my_otu_table, metadata = my_metadata, tree = my_tree)
ps1.av2

# Heatmap
amp_heatmap(ps1.av2, group_by = "day", facet_by = "randomization_arm")

# Boxplot
amp_boxplot(ps1.av2, group_by = "day", tax_add = "Phylum")

```