---
title: "Working with phyloseq"
author: 
  - name: Zachary Kurtz
    email: zdkurtz@gmail.com
output: 
  BiocStyle::html_document:
    self_contained: yes
    toc: true
    toc_float: true
    toc_depth: 2
    code_folding: show
date: "`r format(Sys.time(), '%B %d, %Y')`"
package: "SpiecEasi"
version: "1.99.3"
vignette: >
  %\VignetteIndexEntry{Working with phyloseq}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}  
---

```{r setup, echo = FALSE, eval=TRUE, message=FALSE}
library(BiocStyle)
knitr::opts_knit$set(
  upload.fun = NULL,
  base.url = NULL) # use local files for images
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#"
)
# Override BiocStyle plot hook to avoid css_align issues
knitr::knit_hooks$set(plot = function(x, options) {
  paste0('![', basename(x), '](', x, ')')
})
runchunks = if (Sys.getenv("FORCE_VIGNETTE_REBUILD", "FALSE") == "TRUE") TRUE else FALSE

cache_file <- '../vignette_cache/phyloseq-integration.RData'
if (!runchunks && file.exists(cache_file)) {
  load(cache_file)
  # If we loaded trimmed objects, reassign them to original names
  if (exists("se.mb.amgut2.trimmed")) {
    se.mb.amgut2 <- se.mb.amgut2.trimmed
    rm(se.mb.amgut2.trimmed)
  }
} else {
  if (!runchunks) {
    message("Cache file phyloseq-integration.RData not found - building from scratch")
  }
  runchunks <- TRUE
}
saveout   = runchunks
```

# Working with phyloseq

SpiecEasi includes some convenience wrappers to work directly with `phyloseq` objects.

```{r, eval=TRUE}
library(SpiecEasi)
library(phyloseq)
## Load round 2 of American gut project
data('amgut2.filt.phy')
```


```{r, eval=runchunks, warning=FALSE, message=FALSE}
se.mb.amgut2 <- spiec.easi(amgut2.filt.phy, method='mb', lambda.min.ratio=1e-2,
                           nlambda=20, pulsar.params=list(rep.num=50))
ig2.mb <- adj2igraph(getRefit(se.mb.amgut2),  vertex.attr=list(name=taxa_names(amgut2.filt.phy)))
```


The `plot_network` function provides an easy way to visualize networks with taxonomic information from phyloseq objects. You can specify different taxonomic ranks for coloring nodes and customize the visualization further.
```{r, eval=TRUE}
plot_network(ig2.mb, amgut2.filt.phy, type='taxa', color="Rank3")
```

Session info:
```{r}
sessionInfo()
```

```{r, echo = FALSE, eval=TRUE, message=FALSE}
# Save objects if they exist
if (exists("se.mb.amgut2") && exists("ig2.mb")) {
  cache_file <- '../vignette_cache/phyloseq-integration.RData'
  tryCatch({
    # Load trimming function and trim objects to reduce size
    source('../vignette_cache/trim_spiec_easi.R')
    se.mb.amgut2.trimmed <- trim_spiec_easi(se.mb.amgut2)
    
    # Save trimmed objects
    save(se.mb.amgut2.trimmed, ig2.mb, file=cache_file)
    message("Saved trimmed cache file: ", cache_file, " in directory: ", getwd())
  }, error = function(e) {
    message("Failed to save cache file: ", e$message)
  })
}
``` 