show_table-methods: Display an interactive or static table.

In abrionne/ViSEAGO: ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

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)

abrionne/ViSEAGO documentation built on June 13, 2019, 2:27 p.m.