plotFeaturesHeatmap {PAA} | R Documentation

## Plot feature intensities as a heatmap.

### Description

Plots intensities of given features as a heatmap.

### Usage

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

### Arguments

`features` | vector containing `"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 tiff 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 tiff file in `output.path`. This function can be used to check whether the selected features are differential.

### Value

No value is returned.

### Author(s)

Michael Turewicz, michael.turewicz@rub.de

### 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(features=selectFeatures.results$features, elist=elist,
     n1=20, n2=20, description=TRUE)

[Package PAA version 1.20.0 Index]