Visualise missing values as a heatmap and barplots along the
samples and features.
Usage
naplot(object, verbose = TRUE, ...)
Arguments
object
An object of class MSnSet.
verbose
If verbose (default is TRUE), print a table
of missing values.
...
Additional parameters passed to image2.
Value
Used for its side effect. Invisibly returns NULL
Author(s)
Laurent Gatto
Examples
data(naset)
naplot(naset)
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
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(MSnbase)
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/naplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: naplot
> ### Title: Overview of missing value
> ### Aliases: naplot
>
> ### ** Examples
>
> data(naset)
> naplot(naset)
features.na
0 1 2 3 4 8 9 10
301 247 91 13 2 23 10 2
samples.na
34 39 41 42 43 45 47 49 51 52 53 55 56 57 61
1 1 1 1 1 2 1 1 1 1 1 1 1 1 1
>
>
>
>
>
> dev.off()
null device
1
>