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Last data update: 2014.03.03

R: NA heatmap visualisation for 2 groups

imageNA2

R Documentation

NA heatmap visualisation for 2 groups

Description

Produces a heatmap after reordring rows and columsn to highlight missing value patterns.

Usage

imageNA2(object, pcol, Rowv, Colv = TRUE, useGroupMean = FALSE,
  plot = TRUE, ...)

Arguments

`object`	An instance of class MSnSet
`pcol`	Either the name of a phenoData variable to be used to determine the group structure or a factor or any object that can be coerced as a factor of length equal to nrow(object). The resulting factor must have 2 levels. If missing (default) `image(object)` is called.
`Rowv`	Determines if and how the rows/features are reordered. If missing (default), rows are reordered according to `order((nNA1 + 1)^2/(nNA2 + 1))`, where NA1 and NA2 are the number of missing values in each group. Use a vector of numerics of feautre names to customise row order.
`Colv`	A `logical` that determines if columns/samples are reordered. Default is `TRUE`.
`useGroupMean`	Replace individual feature intensities by the group mean intensity. Default is FALSE.
`plot`	A `logical` specifying of an image should be produced. Default is `TRUE`.
`...`	Additional arguments passed to `image`.

Value

Used for its side effect of plotting. Invisibly returns Rovw and Colv.

Author(s)

Laurent Gatto, Samuel Wieczorek and Thomas Burger

Examples

library("pRolocdata")
library("pRoloc")
data(dunkley2006)
pcol <- ifelse(dunkley2006$fraction <= 5, "A", "B")
nax <- makeNaData(dunkley2006, pNA = 0.10)
exprs(nax)[sample(nrow(nax), 30), pcol == "A"] <- NA
exprs(nax)[sample(nrow(nax), 50), pcol == "B"] <- NA
MSnbase:::imageNA2(nax, pcol)
MSnbase:::imageNA2(nax, pcol, useGroupMean = TRUE)
MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = FALSE)
MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = TRUE)

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.
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Type 'license()' or 'licence()' for distribution details.

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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(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/imageNA2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: imageNA2
> ### Title: NA heatmap visualisation for 2 groups
> ### Aliases: imageNA2
> 
> ### ** Examples
> 
> library("pRolocdata")

This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> library("pRoloc")
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.12.4 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

> data(dunkley2006)
> pcol <- ifelse(dunkley2006$fraction <= 5, "A", "B")
> nax <- makeNaData(dunkley2006, pNA = 0.10)
> exprs(nax)[sample(nrow(nax), 30), pcol == "A"] <- NA
> exprs(nax)[sample(nrow(nax), 50), pcol == "B"] <- NA
> MSnbase:::imageNA2(nax, pcol)
> MSnbase:::imageNA2(nax, pcol, useGroupMean = TRUE)
> MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = FALSE)
> MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>