---
title: "Getting Started with tidypq"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with tidypq}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(tidypq)
library(MiscMetabar)
```

## Overview
tidypq provides tidyverse-style verbs for manipulating phyloseq objects. Use the `.` pronoun to refer to the phyloseq object within expressions.

## Filter samples
```{r}
# By metadata
data_fungi |> 
  filter_samples_pq(Height == "Low")

# By sequencing depth
data_fungi |> 
  filter_samples_pq(sample_sums(.) > 5000)

# Both criteria
data_fungi |> 
  filter_samples_pq(Height == "Low" & sample_sums(.) > 5000)
```

## Filter taxa
```{r}
# By taxonomy
data_fungi |> 
  filter_taxa_pq(Phylum == "Basidiomycota")

# By abundance
data_fungi |> 
  filter_taxa_pq(taxa_sums(.) > 100)
```

## Mutate
```{r}
# Add sample depth
fungi_modif <- data_fungi |> 
  mutate_samdata_pq(depth = sample_sums(.), 
    hill_2 = vegan::renyi(.@otu_table, scales = 2, hill = TRUE),
    )
```

## Select columns
```{r}
# Select sample metadata
data_fungi |> select_samdata_pq(Height, Time)

# Select taxonomic ranks
data_fungi |> select_taxa_pq(Phylum:Genus)
```

## Chaining operations
```{r}
data_fungi |>
  filter_samples_pq(Height == "Low") |>
  filter_taxa_pq(taxa_sums(.) > 50) |>
  mutate_samdata_pq(log_depth = log(sample_sums(.)))
```