netGOTFPlot {CeTF} | R Documentation

## Plot a network for Ontologies, genes and TFs

### Description

Generate the plot of groupGO network result of `getGroupGO` function, and the integrated network of genes, GOs and TFs.

### Usage

    netGOTFPlot(
      netCond,
      resultsGO,
      netGO,
      anno,
      groupBy = "pathways",
      TFs = NULL,
      genes = NULL,
      keyTFs = NULL,
      size = 0.5,
      type = NULL
    )

### Arguments

`netCond` | Network of a specific condition. Can be found in result of `runAnalysis` (see `NetworkData` and `NetworkData`).
`resultsGO` | Dataframe with the results of `getGroupGO` (first element of list). This result can be filtered by applying filters for pathways selection.
`netGO` | Dataframe with the results of `getGroupGO` (second element of list).
`anno` | Annotation of gene or TFs. Can be found in result of `runAnalysis` function (see `NetworkData`).
`groupBy` | Which variables do you want to group in GO type? The options are: 'pathways', 'TFs' and 'genes' (default: 'pathways').
`TFs` | A character with selected TFs.
`genes` | A character with selected genes.
`keyTFs` | TFs identified as importants by `runAnalysis` (see `NetworkData`). This argument is used only if the type argument equals Integrated.
`size` | Size of nodes labels (default: 0.5).
`type` | Type of plot selected (GO or Integrated). If GO will plot the associated GO grouped by some variable, and if Integrated will plot a integrated network with genes, GO and TFs.

### Value

Returns a list with the plot of the network for GO or integrated output under a condition and the table used to plot the network.

### Examples

    ## Not run:
    # load the annotation package
    library(org.Hs.eg.db)

    # load the CeTF class object resulted from runAnalysis function
    data(CeTFdemo)

    # getting the genes in network of condition 1
    genes <- unique(c(as.character(NetworkData(CeTFdemo, 'network1')[, 'gene1']),
                     as.character(NetworkData(CeTFdemo, 'network1')[, 'gene2'])))

    # performing getGroupGO analysis
    cond1 <- getGroupGO(genes = genes,
                        ont = 'BP',
                        keyType = 'ENSEMBL',
                        annoPkg = org.Hs.eg.db,
                        level = 3)

    # selecting only first 12 pathways
    t1 <- head(cond1$results, 12)

    # subsetting the network to have only the first 12 pathways
    t2 <- subset(cond1$netGO, cond1$netGO$gene1 %in% as.character(t1[, 'ID']))

    # generate the GO plot grouping by pathways
    pt <- netGOTFPlot(netCond = NetworkData(CeTFdemo, 'network1'),
                  resultsGO = t1,
                  netGO = t2,
                  anno = NetworkData(CeTFdemo, 'annotation'),
                  groupBy = 'pathways',
                  keyTFs = NetworkData(CeTFdemo, 'keytfs'),
                  type = 'GO')
    pt$plot
    head(pt$tab$`GO:0006807`)

    # generate the Integrated plot
    pt <- netGOTFPlot(netCond = NetworkData(CeTFdemo, 'network1'),
                  resultsGO = t1,
                  netGO = t2,
                  anno = NetworkData(CeTFdemo, 'annotation'),
                  groupBy = 'pathways',
                  keyTFs = NetworkData(CeTFdemo, 'keytfs'),
                  type = 'Integrated')
    pt$plot
    head(pt$tab)

    ## End(Not run)

[Package CeTF version 1.2.4 Index]