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