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man/plot.seqinsample.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.seqinsample.R
+\name{plot.seqinsample}
+\alias{plot.seqinsample}
+\title{Plot sequence abundance in samples}
+\usage{
+\method{plot}{seqinsample}(x, seqset, seqtype, controls = NULL)
+}
+\arguments{
+\item{x}{a \code{\link{metabarcoding.data}} object}
+
+\item{seqset}{a vetcor with sequences names}
+
+\item{seqtype}{a string indicating what type of sequences are displayed}
+
+\item{controls}{a vector indicating the negative controls names in the x object.
+Default is \code{NULL}}
+}
+\value{
+returns a plot with the log10 transformed relative porportion of 
+        selected MOTUs in each samples. If the number of samples is > 96,
+        then the plot is displayed in 4 panels
+}
+\description{
+Plots relative abundances of a set of sequences in all samples (log10 transformed)
+}
+\examples{
+
+data(termes)
+
+seqset = rownames(termes$motus)[which(termes$motus$genus_name=="Anoplotermes")]
+plot.seqinsample(termes, seqset, "Anoplotermes")
+
+controls = rownames(termes)[grep("r", rownames(termes))]
+seqset = rownames(termes$motus)[which(termes$motus$best_identity<0.7)]
+plot.seqinsample(termes, seqset, "Not assigned", controls)
+
+}
+\seealso{
+\code{\linkS4class{taxonomy.obitools}}, and method \code{\link{taxonmicank}}
+}
+\author{
+Lucie Zinger
+}
+\keyword{metabarcoding}