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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# speedyseq
<!-- badges: start -->
[](https://zenodo.org/badge/latestdoi/179732395)
[](https://travis-ci.com/mikemc/speedyseq)
[](https://codecov.io/gh/mikemc/speedyseq?branch=main)
<!-- badges: end -->
Speedyseq is an R package for microbiome data analysis that extends the popular [phyloseq](https://joey711.github.io/phyloseq/) package. Speedyseq began with the limited goal of providing faster versions of phyloseq's plotting and taxonomic merging functions, but now contains a growing number of enhancements to phyloseq which I have found useful.
## Installation
Install the current development version with the remotes package,
```{r, eval = FALSE}
# install.packages("remotes")
remotes::install_github("mikemc/speedyseq")
```
## Usage
Method 1: Call speedyseq functions explicitly when you want to use speedyseq's version instead of phyloseq. This method ensures that you do not unintentionally call speedyseq's version of a phyloseq function.
```{r}
library(phyloseq)
data(GlobalPatterns)
system.time(
# Calls phyloseq's psmelt
df1 <- psmelt(GlobalPatterns) # slow
)
system.time(
df2 <- speedyseq::psmelt(GlobalPatterns) # fast
)
dplyr::all_equal(df1, df2, ignore_row_order = TRUE)
detach(package:phyloseq)
```
Method 2: Load speedyseq, which will load phyloseq and all speedyseq functions and cause calls to the overlapping function names to go to speedyseq by default.
```{r}
library(speedyseq)
data(GlobalPatterns)
system.time(
ps1 <- phyloseq::tax_glom(GlobalPatterns, "Genus") # slow
)
system.time(
# Calls speedyseq's tax_glom
ps2 <- tax_glom(GlobalPatterns, "Genus") # fast
)
```
Loading speedyseq will also load the [magrittr](https://magrittr.tidyverse.org/) pipe (`%>%`) to allow pipe chains with phyloseq objects,
```{r}
gp.filt.prop <- GlobalPatterns %>%
filter_taxa2(~ sum(. > 0) > 5) %>%
transform_sample_counts(~ . / sum(.))
```
## Features
### Faster implementations of phyloseq functions
* `psmelt()` and the plotting functions that use it: `plot_bar()`, `plot_heatmap()`, and `plot_tree()`.
* The taxonomic merging functions `tax_glom()` and `tip_glom()`. Speedyseq's `tip_glom()` also has significantly lower memory usage.
These functions should generally function as drop-in replacements for phyloseq's versions, with additional arguments allowing for modified behavior. Differences in row order (for `psmelt()`) and taxon order (for `tax_glom()`) can occur; see [Changelog](https://mikemc.github.io/speedyseq/news/index.html) for details.
### New taxonomic merging functions
* A general-purpose merging function `merge_taxa_vec()` that provides a vectorized version of phyloseq's `merge_taxa()` function.
* A function `tree_glom()` that performs direct phylogenetic merging of taxa. This function provides an alternative to the indirect phylogenetic merging done by `tip_glom()` that is much faster and arguably more intuitive.
See the [Changelog](https://mikemc.github.io/speedyseq/news/index.html) for details and examples.
### Enhancements and additions to other phyloseq functions
See the [online documentation](https://mikemc.github.io/speedyseq/reference/index.html) for an up-to-date list and usage information and the [Changelog](https://mikemc.github.io/speedyseq/news/index.html) for further information.