show_table {ViSEAGO} | R Documentation

## Display an interactive or static table.

### Description

This method is used to display or print the table for `enrich_GO_terms-class` or `GO_clusters-class` objects.

### Usage

    show_table(object, file = NULL)

    ## S4 method for signature 'ANY'
    show_table(object, file = NULL)

### Arguments

`object` | an `enrich_GO_terms-class` object from `merge_enrich_terms`, or `GO_clusters-class` object from `GOterms_heatmap`.
`file` | table output file name (default to NULL).

### Details

This method displays an interactive table (if file=NULL) from `enrich_GO_terms-class` or `GO_clusters-class` objects.
The table could be printed by setting file argument.

### Value

display or print table

### References

Yihui Xie (2016). DT: A Wrapper of the JavaScript Library 'DataTables'. R package version 0.2. https://CRAN.R-project.org/package=DT

### See Also

Other enrich_GO_terms: `Upset`, `enrich_GO_terms-class`, `overLapper`, `show_heatmap`

Other GO_clusters: `GO_clusters-class`, `GOclusters_heatmap`, `clusters_cor`, `compare_clusters`, `show_heatmap`

Other visualization: `GOclusters_heatmap`, `GOcount`, `GOterms_heatmap`, `Upset`, `available_organisms`, `overLapper`, `show_heatmap`

### Examples

    ###################
    # load example object
    data(
        myGOs,
        package="ViSEAGO"
    )

    ###################
    # display merge_enrich_terms output
    ViSEAGO::show_table(myGOs)

    ###################
    # print merge_enrich_terms output
    ViSEAGO::show_table(
        myGOs,
        "myGOs.txt"
    )

    ## Not run:
    ###################
    # compute GO terms Semantic Similarity distances
    myGOs<-ViSEAGO::compute_SS_distances(
        distance="Wang"
    )

    ##################
    # GOtermsHeatmap with default parameters
    Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
        myGOs,
        showIC=TRUE,
        showGOlabels=TRUE,
        GO.tree=list(
            tree=list(
                distance="Wang",
                aggreg.method="ward.D2",
                rotate=NULL
            ),
            cut=list(
                dynamic=list(
                    pamStage=TRUE,
                    pamRespectsDendro=TRUE,
                    deepSplit=2,
                    minClusterSize =2
                )
            )
        ),
        samples.tree=NULL
    )
    ###################
    # display table of GO_clusters-class object
    ViSEAGO::show_table(Wang_clusters_wardD2)

    ###################
    # print table of GO_clusters-class object
    ViSEAGO::show_table(
        Wang_clusters_wardD2,
        "Wang_clusters_wardD2.txt"
    )

    ## End(Not run)

[Package ViSEAGO version 1.0.0 Index]