plot_condition: Plot DNA concentrations as a function of experimental...

In decontam: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Description

Plots DNA concentration as a function of experimental conditions. This function is intended as a convenient exploration of potential covariation between DNA concentrations and conditions that could influence the community composition, as this could lead to higher rates of false-positive contaminant identifications.

Usage

plot_condition(seqtab, condition, conc, batch = NULL, log = FALSE)

Arguments

seqtab	(Required). Integer matrix or phyloseq object. A feature table recording the observed abundances of each sequence feature (e.g. OTUs or ASVs or or genus or ortholog or...) in each sample. Rows should correspond to samples, and columns to sequences (or OTUs). If a phyloseq object is provided, the otu-table component will be extracted.
condition	(Required). numeric or any type coercible to a factor. Default NULL. If provided, should be a vector of length equal to the number of input samples which specifies the experimental condition of interest for each sample (e.g. pH). If seqtab was provided as a phyloseq object, the name of the appropriate sample-variable in that phyloseq object can be provided.
conc	(Required). numeric. A quantitative measure of the concentration of amplified DNA in each sample prior to sequencing. All values must be greater than zero. Zero is assumed to represent the complete absence of DNA. If seqtab was provided as a phyloseq object, the name of the sample variable in the phyloseq object can be provided.
batch	(Optional). factor, or any type coercible to a factor. Default NULL. If provided, should be a vector of length equal to the number of input samples which specifies which batch each sample belongs to (eg. sequencing run). Contaminants identification will be performed independently within each batch. If seqtab was provided as a phyloseq object, the name of the appropriate sample-variable in that phyloseq object can be provided.
log	(Optional). logical. Default TRUE. If TRUE, the axes are log10-scaled.

Examples

# MUC is a phyloseq object, MUC.conc is the vector of sample concentrations
MUC <- readRDS(system.file("extdata", "MUClite.rds", package="decontam"))
MUC.conc <- readRDS(system.file("extdata", "MUCconc.rds", package="decontam"))
plot_condition(MUC, "Habitat", MUC.conc)
# Plot against random quantitative variable
plot_condition(MUC, runif(length(MUC.conc)), MUC.conc, log=TRUE)

decontam documentation built on Nov. 8, 2020, 10:58 p.m.