plotFeaturesHeatmap.2 {PAA} | R Documentation

## Alternative function to plot feature intensities as a heatmap.

### Description

This function is an alternative to `plotFeaturesHeatmap()` and is based on the function `heatmap.2()` provided by the package `gplots`.

### Usage

    plotFeaturesHeatmap.2(features = NULL, elist = NULL, n1 = NULL, n2 = NULL,
     output.path = NULL, description=FALSE)

### Arguments

`features` | vector containing the selected features as `"BRC"`-IDs (mandatory).
`elist` | `EListRaw` or `EList` object containing all intensity data in log2 scale (mandatory).
`n1` | integer indicating the sample size of group 1 (mandatory).
`n2` | integer indicating the sample size of group 2 (mandatory).
`output.path` | path for saving the heatmap as a png file (default: NULL).
`description` | if TRUE, features will be described via protein names instead of UniProtKB accessions (default: FALSE).

### Details

Plots intensities of all features given in the vector `features` via their corresponding `"BRC"`-IDs as a heatmap. If `description` is TRUE (default: FALSE), features will be described via protein names instead of UniProtKB accessions. Furthermore, if `output.path` is not NULL, the heatmap will be saved as a png file in `output.path`. This function can be used to check whether the selected features are differential.

`plotFeaturesHeatmap.2()` is an alternative to `plotFeaturesHeatmap()` and is based on the function `heatmap.2()` provided by the package `gplots`.

### Value

No value is returned.

### Author(s)

Ivan Grishagin (Rancho BioSciences LLC, San Diego, CA, USA), John Obenauer (Rancho BioSciences LLC, San Diego, CA, USA) and Michael Turewicz (Ruhr-University Bochum, Bochum, Germany), michael.turewicz@rub.de

### References

The package `gplots` by Gregory R. Warnes et al. can be downloaded from CRAN (http://CRAN.R-project.org/package=gplots).

Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber, Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2015). gplots: Various R Programming Tools for Plotting Data. R package version 2.17.0. http://CRAN.R-project.org/package=gplots

### Examples

    cwd <- system.file(package="PAA")
    load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
    #elist <- elist[elist$genes$Block < 10,]

    #c1 <- paste(rep("AD",20), 1:20, sep="")
    #c2 <- paste(rep("NDC",20), 1:20, sep="")

    #pre.sel.results <- preselect(elist=elist, columns1=c1, columns2=c2, label1="AD",
    # label2="NDC", discard.threshold=0.1, fold.thresh=1.9, discard.features=TRUE,
    # method="tTest")
    #elist <- elist[-pre.sel.results$discard,]

    #selectFeatures.results <- selectFeatures(elist,n1=20,n2=20,label1="AD",
    # label2="NDC",selection.method="rf.rfe",preselection.method="none",subruns=2,
    # k=2,candidate.number=20,method="frequency")

    load(paste(cwd, "/extdata/selectFeaturesResultsFreq.RData", sep=""))
    plotFeaturesHeatmap.2(features=selectFeatures.results$features, elist=elist,
     n1=20, n2=20, description=TRUE)

[Package PAA version 1.28.0 Index]