62 lines
2.2 KiB
R
62 lines
2.2 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/distrib.extrapol.R
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\name{map.extrapol.freq}
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\alias{map.extrapol.freq}
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\title{Maps of krigged log10-transformed frequencies}
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\usage{
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map.extrapol.freq(x, path = NULL, col.name = NULL, index, cutoff = 0.001,
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add.points = NULL, adj = 4)
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}
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\arguments{
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\item{x}{an extrapol.freq output}
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\item{path}{the path of the folder to export the map. Default is \code{NULL} and map is printed in Rplot/quartz}
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\item{index}{an integer indicating column number of the motu/sequence to be plotted.}
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\item{cutoff}{lower motu frequency accepted to consider motu abundance as different
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from 0. Should be the same than the one used in extrapol.freq}
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\item{add.points}{a 3-column data.frame containing factor levels and associated x and y coordinates
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to be added to the map. Typically taxa observed in the field.}
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\item{adj}{a value used for adjusting text position in the map. Default is \code{4}}
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\item{col.names}{a vector containing the names of the columns to be used for defining the file name. Typically
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the column names containing the taxonomic information and/or sequence/motus id.}
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}
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\value{
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a map/png file displaying motus distribution.
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}
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\description{
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Maps the output of extrapol.freq
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}
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\examples{
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data(termes)
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attr(termes, "samples")[c("x", "y")] = expand.grid(1:7,1:3)
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#compute frequencies
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attr(termes, "layers")[["reads.freq"]] = normalize(termes, MARGIN=1)$reads
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# Getting extrapolations
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termes.pred = extrapol.freq(attr(termes, "layers")[["reads.freq"]],
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grid.grain=100,termes$samples[,c("x", "y")], termes$motus, cutoff=1e-3)
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#mapping the distribution of the 3 most abundant sequences (caution, mfrow does not work for lattice's levelplot)
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map.extrapol.freq(termes.pred, path=NULL, col.name=NULL, 1, cutoff=1e-3)
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map.extrapol.freq(termes.pred, path=NULL, col.name=NULL, 2, cutoff=1e-3)
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map.extrapol.freq(termes.pred, path=NULL, col.name=NULL, 3, cutoff=1e-3)
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#dummy observationnal data
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termes.obs = data.frame(x=c(2,3,5), y=c(2.7,2,2.6), taxa = rep("Isoptera Apicotermitinae", 3))
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map.extrapol.freq(termes.pred, path=NULL, col.name=NULL, 3, cutoff=1e-3, add.points=termes.obs)
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}
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\seealso{
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\code{\link{extrapol.freq}}, and \code{levelplot} from \code{lattice} package
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}
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\author{
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Lucie Zinger
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}
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