---
title: "Advanced Usage"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Advanced Usage}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

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

## Custom functions in filter

```{r}
# Filter taxa present in at least 3 samples
data_fungi |> 
  filter_taxa_pq(taxa_prevalence(.) >= 3)

# Filter samples with above-median depth
data_fungi |>
   filter_samples_pq(sample_sums(.) > median(sample_sums(.)))
```

## Custom functions in mutate

```{r}
# Prevalence ratio
data_fungi |> mutate_taxa_pq(
  prev_ratio = taxa_prevalence(.) / nsamples(.)
)

# Relative abundance rank
data_fungi |> mutate_taxa_pq(
  abundance_rank = rank(-taxa_sums(.))
)
```

## Occurrence-level transformations

```{r}
# Relative abundance
data_fungi |> mutate_occurrences_pq(. / sample_total)

# Filter low-abundance occurrences
data_fungi |> filter_occurrences_pq(. / sample_total > 0.001)
```

## Complex pipelines

```{r}
data_fungi |>
  filter_samples_pq(sample_sums(.) > quantile(sample_sums(.), 0.25)) |>
  filter_taxa_pq(taxa_prevalence(.) >= 2, taxa_sums(.) > 10) |>
  mutate_taxa_pq(
    prevalence = taxa_prevalence(.),
    mean_abundance = taxa_sums(.) / nsamples(.)
  ) |>
  mutate_occurrences_pq(. / sample_total)
```