Introduction to the archaeacentre package

Richard Stöckl

Archaea Centre Regensburg

12 February 2025

Source: vignettes/archaeacentre.Rmd

Basics

Install archaeacentre

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. biocthis is a R package available via the Github repository.

Get the latest stable R release from CRAN. Then install the development of archaeacentre from GitHub with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install(c("remotes", "richardstoeckl/archaeacentre"))

Presets for growth curves of microbial growth data

Plot a basic growth curve 

# 1. load the package
library(archaeacentre)

# 2. load some test data included with the package
testData <- archaeacentre::growthData

# 3. plot the growth curves in their most basic way, with the presets for "robert":
archaeacentre::plotGrowthCurve(testData, timepoint, concentration, grouping = c("timepoint", "organism"), organism, type = "robert")

Modify your growth curve plot

Since the plotGrowthCurve function is basically just a wrapper around a ggplot2 plot with some default settings, you can modify the plot to your liking. Here is one example:

library(ggplot2)

archaeacentre::plotGrowthCurve(testData, timepoint, concentration, grouping = c("timepoint", "organism"), organism, type = "robert") +
    ggplot2::labs(title = "Growth curve of some test data", x = "Timepoint after inocculation in [h]", y = "Concentration in [cells/mL]") +
    ggplot2::guides(color = guide_legend(title = "Species")) +
    ggplot2::facet_grid(~organism)

Get PDB Annotation data for a given PDB filename as returned by Foldseek

is a fast search tool for comparing protein structures. When searching for similar structures in the PDB, Foldseek returns a table which contains the “target” column. In the case of searches against the PDB, this target column contains the PDB filename of the hit, which is not easily interpretable.

The provides structural and functional annotations for macromolecules stored in the Protein Data Bank (PDB).

The get_pfam_annotation_for_targets() function automates the extraction of Pfam domain annotations for these target PDB filenames returned by Foldseek,using the .

# Get a vector of PDB filenames. This could be the "target" column of a Foldseek search result table.
targets <- c("1U04_assembly1.cif_A", "8HL4_assembly1.cif_L18P")
# Get the Pfam annotations for these targets. As the RCSB API has a rate limit, we recommend to use a batch size of 1000 or lower.
pfam_results <- get_pfam_annotation_for_targets(targets, batch_size = 1000)
head(pfam_results)
#> # A tibble: 2 × 4
#>   target                  rcsb_id title                         pfam_description
#>   <chr>                   <chr>   <chr>                         <chr>           
#> 1 1U04_assembly1.cif_A    1U04.A  Crystal structure of full le… Argonaute, N-te…
#> 2 8HL4_assembly1.cif_L18P 8HL4.Q  Cryo-EM Structures and Trans… Ribosomal large…