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man/plot.PCRplate.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.PCRplate.R
+\name{plot.PCRplate}
+\alias{plot.PCRplate}
+\title{Plot PCR plates}
+\usage{
+\method{plot}{PCRplate}(x, samples = NULL, col = "cyan2", different = T,
+  ...)
+}
+\arguments{
+\item{x}{a \code{\link{metabarcoding.data}} object}
+
+\item{samples}{a character vector containing names of problematic samples. Default is \code{NULL}}
+
+\item{different}{a boolean indicating whether different tags where used in forward and reverse to identify samples. Default is \code{TRUE}}
+
+\item{...}{arguments ot be passed to methods, such as graphical parameters}
+}
+\value{
+\code{\link{plot.PCRplate}} returns a plot displaying no more than 4 PCR plates, with problematic sample localization
+}
+\description{
+Plots samples localization in PCR plates, and points out problematic samples if provided.
+}
+\examples{
+\dontshow{# switch the working directory to the data package directory}
+\dontshow{setwd(system.file("extdata", package="ROBITools"))}
+
+data(termes)
+
+# reading the termes_ngsfilt.txt file
+termes.ngs=import.ngsfilter.data('termes_ngsfilt.txt', platewell="position")
+
+# including ngsfilter data into termes data
+attr(termes, "samples") = termes.ngs[rownames(termes),]
+
+#plot PCR plate plan
+col = rep("green", nrow(termes))
+col[grep("r", rownames(termes))] = "red"
+plot.PCRplate(termes, col=col)
+
+#highlighting location of samples with low identification score
+
+#low quality taxonomic assignements identification
+library(plotrix)
+weighted.hist(termes$motus$best_identity, colSums(termes$reads), breaks = 20, ylab = "Nb reads", xlab = "Ecotag scores", xaxis=F)
+axis(1, labels = T)
+lowqual.seq = rownames(termes$motus)[termes$motus$best_identity < 0.7]
+
+#identification and localization (in PCR plate) of samples with high proportions of low quality taxonomic assignements
+termes.freq= normalize(termes, MARGIN=1)$reads
+hist(log10(rowSums(termes.freq[,lowqual.seq]) + 1e-05), breaks = 20, xlab = "Prop low quality reads")
+lowqual.sample = rownames(termes)[log10(rowSums(termes.freq[, lowqual.seq]) + 1e-05) > -0.5]
+
+plot.PCRplate(termes, lowqual.sample, col=col)
+  
+}
+\seealso{
+\code{\link{import.metabarcoding.data}}
+}
+\author{
+Lucie Zinger
+}
+\keyword{DNA}
+\keyword{metabarcoding}