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Ampvis

An R package to visualise amplicon data

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Installation

Install the latest version of R, Rtools and Rstudio.

A few packages needs to be installed through RStudio before ampvis can be installed. Make sure you run RStudio as Administrator to enable installation of all packages! If you are asked to update packages, then press "a" for all.

install.packages("devtools")
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
biocLite("DESeq2")
biocLite("phyloseq")
biocLite("munsell")
biocLite("stringi")
biocLite("chron")
biocLite("permute")
biocLite("assertthat")
biocLite("tibble")
biocLite("rmarkdown")
biocLite("readxl")

Ampvis is installed directly from github using the devtools package.

library("devtools")
install_github("MadsAlbertsen/ampvis")

To cite ampvis in publications, or otherwise credit, please use:

Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH and Nielsen PH. (2015) Back to Basics - The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS ONE 10(7):e0132783.

Examples

First time users of ampvis should start with the basic guide. The associated Rmarkdown file can be downloaded here.

Papers using ampvis

Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH and Nielsen PH. (2015) Back to Basics - The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS ONE 10(7):e0132783.

The processed data from Albertsen et al. (2015) is included directly in ampvis as data(DNAext_1.0). All ampvis figures from the paper can be recreated using the Rmarkdown files:

Figure 1 (Rmd), Figure 2 (Rmd), Figure 3A (Rmd), Figure 3B (Rmd), Figure 4A (Rmd), Figure 4B (Rmd), Figure 5A (Rmd), Figure 5B (Rmd), Figure 6A (Rmd), Figure 6B (Rmd)

Figure S1 (Rmd), Figure S2 (Rmd), Figure S3 (Rmd), Figure S4 (Rmd), Figure S5 (Rmd), Figure S6 (Rmd), Figure S7 (Rmd), Figure S8 (Rmd), Figure S9 (Rmd), Figure S10 (Rmd)

McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL and Nielsen, P. H. (2015). MiDAS: the field guide to the microbes of activated sludge. Database: bav062

The processed data from McIlroy et al. (2015) is included directly in ampvis as data (MiDAS_1.20). All ampvis figures from the paper can be recreated using the Rmarkdown files:

Figure 1 (Rmd)