Overview
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Install and load the R packages we need to run the analysis
Import our taxonomic abundance table into R
View a summary of our abundance table
Install required R packages
Copy We’re going to be running various commands in R. To do this, copy and paste the following code into the R script you just created, then run the code ( highlight all the code in your R scriptyou want to run, then press the run button). This will install all the required packages and :
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Install required R packages
Copy and paste the following code into the R script you just created, then run the code. This will install all the required packages and dependencies and may take 45 minutes or more to complete. It may prompt you occasionally to update packages - select 'a' for all if/when this occurs.
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NOTE: you only need to run this section once if you’re running this analysis on your own laptop/PC, and you don’t need to run it if you’re using an rVDI machine as all the packages are already installed.
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#### Metagenomics analysis ####
# When you see '## USER INPUT', this means you have to modify the code for your computer or dataset. All other code can be run as-is (i.e. you don't need to understand the code, just run it)
#### 1. Installing required packages ####
# **NOTE: this section only needs to be run once (or occasionally to update the packages)
# Install devtools
install.packages("devtools", repos = "http://cran.us.r-project.org")
# Install R packages. This only needs to be run once.
# Make a vector of CRAN and Bioconductor packages
bioconductor_packages <- c("VariantAnnotation", "biomaRt", "clusterProfiler", "org.Hs.eg.db")
cran_packages <- c("devtools", "tidyverse", "DT", "gt", "openxlsx", "dplyr", "scales", "ggplot2", "plotly", "tidyr", "ggsci", "viridis", "vcfR", "data.table", "remotes")
# Compares installed packages to above packages and returns a vector of missing packages
new_packages <- bioconductor_packages[!(bioconductor_packages %in% installed.packages()[,"Package"])]
new_cran_packages <- cran_packages[!(cran_packages %in% installed.packages()[,"Package"])]
# Install missing bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(new_packages)
# Install missing cran packages
if (length(new_cran_packages)) install.packages(new_cran_packages, repos = "http://cran.us.r-project.org")
# Update all installed packages to the latest version
update.packages(bioconductor_packages, ask = FALSE)
update.packages(cran_packages, ask = FALSE, repos = "http://cran.us.r-project.org")
# Install ampvis2 (needs to be installed from Github)
remotes::install_github("kasperskytte/ampvis2")
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Load required R packages
This section loads the packages you’ve installed in the previous section. Unlike installing packages, this needs to be run every time and should only take a few seconds to run.
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#### 32. Loading required packages #### # This section needs to be run every time # Load packages bioconductor_packages <- c("DESeq2VariantAnnotation", "biomaRt", "EnhancedVolcanoclusterProfiler", "org.Hs.eg.db", "org.Mm.eg.db) cran_packages <- c("devtools", "org.Rn.eg.dbtidyverse", "org.EcK12.eg.dbDT", "org.EcSakai.eg.dbgt", "org.Dr.eg.dbopenxlsx", "org.Dm.eg.db") cran_packages <- c("ggrepeldplyr", "scales", "ggplot2", "ggplot2plotly", "plyrtidyr", "reshape2ggsci", "readxlviridis", "FactoMineRvcfR", "factoextradata.table", "pheatmapremotes") lapply(cran_packages, require, character.only = TRUE) lapply(bioconductor_packages, require, character.only = TRUE) library(ampvis2) |
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Import your data files into R
In this section, we will import your count table and samples table into R.
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