plot2D {RDAVIDWebService} | R Documentation

## Visualization of biological relationships

### Description

`plot2D` uses a 2D tile ggplot to explore biological relationships between two variables such as annotation category and genes, for Functional Annotation Chart/Table or Term cluster results. For Gene cluster, the cluster number vs genes membership is plotted.

### Usage

      plot2D(object,...)

      ## S4 method for signature 'DAVIDResult'
    plot2D(object, dataFrame)

      ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
    plot2D(object,color=c("FALSE"="black",
      "TRUE"="green"))

      ## S4 method for signature 'DAVIDGeneCluster'
    plot2D(object,color=c("FALSE"="black","TRUE"="green"),names=FALSE)

      ## S4 method for signature 'DAVIDTermCluster'
    plot2D(object,number=1,color=c("FALSE"="black","TRUE"=
      "green"))

      ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
    plot2D(object,
      category, id, names.genes=FALSE,
      names.category=FALSE,color=c("FALSE"="black","TRUE"="green"))

### Arguments

`object` | DAVIDResult heirs (DAVIDFunctionalAnnotationChart/Table or DAVIDGeneCluster/TermCluster)
`dataFrame` | data.frame with three columns (x, y and fill) to be used in ggplot. X(Y) is a character/factor with the X(Y)-axis labels and "fill" is a the color to be used for x-y labels.
`color` | named character vector to indicate tile color. Default value is c("FALSE"="black", "TRUE"="green").
`names` | should gene names be plotted? Default value is FALSE, i.e, use ids.
`number` | integer to indicate which cluster to plot. Default value is 1.
`category` | character vector to select the main annotation categories. By default is missing in order to use all the available ones.
`id` | character vector to indicate which gene ids to use. By default is missing in order to use all the available ones.
`names.genes,names.category` | Should genes and/or category names used? Default value is FALSE, i.e., use both ids.
`...` | Additional parameters for heirs functions.

### Value

a ggplot object if the object is not empty.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### See Also

Other DAVIDFunctionalAnnotationChart: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart-class`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `categories`, `categories`, `categories`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`

Other DAVIDFunctionalAnnotationTable: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable-class`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `categories`, `categories`, `categories`, `dictionary`, `dictionary`, `genes`, `genes`, `genes`, `genes`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `membership`, `membership`, `subset`, `subset`

Other DAVIDGeneCluster: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGeneCluster-class`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `genes`, `genes`, `genes`, `genes`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`

Other DAVIDResult: `DAVIDResult-class`, `type`, `type`

Other DAVIDTermCluster: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `DAVIDTermCluster-class`, `as`, `as`, `as`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`

### Examples

    {
    ##DAVIDFunctionalAnnotationChart example:
    ##Load the Functional Annotation Chart file report for the input demo
    ##file 2, using data function. Just to keep it simple, for the first five
    ##terms present in funChart2 object, create a DAVIDFunctionalAnnotationChart
    ##object and plot a 2D tile matrix with the reported evidence (green) or not
    ##(black).
    data(funChart2)
    plot2D(DAVIDFunctionalAnnotationChart(funChart2[1:5, ]),
    color=c("FALSE"="black", "TRUE"="green"))

    ##DAVIDFunctionalAnnotationTable example
    ##Load the Functional Annotation Table file report for the input demo
    ##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
    ##object using the loaded data.frame annotationTable1.
    data(annotationTable1)
    davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)

    ##Plot the membership of only for the first six terms in this
    ##category, with only the genes of the first six terms with at least one
    ##evidence code.
    ##Category filtering...
    categorySelection<-list(head(dictionary(davidFunTable1,
    categories(davidFunTable1)[1])$ID))
    names(categorySelection)<-categories(davidFunTable1)[1]

    ##Gene filter...
    id<-membership(davidFunTable1, categories(davidFunTable1)[1])[,1:6]
    id<-ids(genes(davidFunTable1))[rowSums(id)>0]

    ##Finally the membership tile plot
    plot2D(davidFunTable1, category=categorySelection, id=id,
    names.category=TRUE)

    ##DAVIDGeneCluster example:
    ##Load the Gene Functional Classification Tool file report for the
    ##input demo list 1 file to create a DAVIDGeneCluster object.
    setwd(tempdir())
    fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
    package="RDAVIDWebService")
    untar(fileName)
    davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))

    ##We can inspect a 2D tile membership plot, to visual inspect for
    ##overlapping of genes across the clusters. Or use an scaled version of gene
    ##names to see the association of gene cluster, e.g., cluster 3 is related to
    ##ATP genes.
    plot2D(davidGeneCluster1)
    plot2D(davidGeneCluster1,names=TRUE)+
    theme(axis.text.y=element_text(size=rel(0.9)))

    ##DAVIDTermCluster example:
    ##Load the Gene Functional Classification Tool file report for the
    ##input demo file 2 to create a DAVIDGeneCluster object.
    setwd(tempdir())
    fileName<-system.file("files/termClusterReport2.tab.tar.gz",
    package="RDAVIDWebService")
    untar(fileName)
    davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))

    ##Finally, we can inspect a 2D tile membership plot, to visual inspect for
    ##overlapping of genes across the term members of the selected cluster,
    ##e.g., the first cluster .
    plot2D(davidTermCluster2, number=1)
    }

[Package RDAVIDWebService version 1.18.0 Index]