plotFeatures {PAA} | R Documentation

## Plot intensities of features.

### Description

Plots intensities of all given features (one sub-plot per feature) in group- specific colors.

### Usage

    plotFeatures(features = NULL, elist = NULL, n1 = NULL, n2 = NULL,
     group1 = "group1", group2 = "group2", output.path = NULL)

### 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).
`group1` | class label of group 1.
`group2` | class label of group 2.
`output.path` | string indicating the folder where the figure will be saved (optional).

### Details

Plots intensities of given features (e.g., selected by the function `selectFeatures()`) in group-specific colors (one sub-plot per feature). All sub-plots are aggregated to one figure. When the argument `output.path` is not NULL this figure will be saved in 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=""))
    plotFeatures(features=selectFeatures.results$features, elist=elist, n1=20,
     n2=20, group1="AD", group2="NDC")

[Package PAA version 1.16.0 Index]