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