Plot of rarefaction effect

Description

This function plots the number of observed features vs. the depth of coverage.

Usage

plotRare(obj, cl = NULL, ...)

Arguments

Value

Library size and number of detected features

See Also

plotOrd, plotMRheatmap, plotCorr, plotOTU, plotGenus

Examples

data(mouseData)
cl = factor(pData(mouseData)[,3])
res = plotRare(mouseData,cl=cl,ret=TRUE,pch=21,bg=cl)
tmp=lapply(levels(cl), function(lv) lm(res[,"ident"]~res[,"libSize"]-1, subset=cl==lv))
for(i in 1:length(levels(cl))){
   abline(tmp[[i]], col=i)
}
legend("topleft", c("Diet 1","Diet 2"), text.col=c(1,2),box.col=NA)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(metagenomeSeq)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metagenomeSeq/plotRare.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRare
> ### Title: Plot of rarefaction effect
> ### Aliases: plotRare
> 
> ### ** Examples
> 
> 
> data(mouseData)
> cl = factor(pData(mouseData)[,3])
> res = plotRare(mouseData,cl=cl,ret=TRUE,pch=21,bg=cl)
Warning messages:
1: In plot.window(...) : "ret" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "ret" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
  "ret" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
  "ret" is not a graphical parameter
5: In box(...) : "ret" is not a graphical parameter
6: In title(...) : "ret" is not a graphical parameter
> tmp=lapply(levels(cl), function(lv) lm(res[,"ident"]~res[,"libSize"]-1, subset=cl==lv))
> for(i in 1:length(levels(cl))){
+    abline(tmp[[i]], col=i)
+ }
> legend("topleft", c("Diet 1","Diet 2"), text.col=c(1,2),box.col=NA)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>