Visualize the results of an enrichment analysis as word cloud

Visualize the results of an enrichment analysis as a word cloud. The word cloud highlights the most frequent terms associated with the description of the genesets in the enrichment analysis.

enrichmentWordcloud(genesets_df)

Arguments

genesets_df

A data.frame object of an enrichment analysis results. This object should follow the input requirements of GeDi(), check out the vignette for further details. Besides the specified required columns, the object should ideally include a column with a short geneset description which is used for the word cloud. If no such column is available, the row names of the data.frame are used for the word cloud.

Value

A wordcloud2::wordcloud2() plot object

Examples

## Mock example showing how the data should look like

## If no "Term" or "Description" column is available,
## the rownames of the data frame will be used.
geneset_df <- data.frame(
              Genesets = c("GO:0002503", "GO:0045087", "GO:0019886"),
              Genes = c("B2M, HLA-DMA, HLA-DMB",
                        "ACOD1, ADAM8, AIM2",
                        "B2M, CD74, CTSS")
)
rownames(geneset_df) <- geneset_df$Genesets

wordcloud <- enrichmentWordcloud(geneset_df)

## With available "Term" column.
geneset_df <- data.frame(
              Genesets = c("GO:0002503", "GO:0045087", "GO:0019886"),
              Genes = c("B2M, HLA-DMA, HLA-DMB",
                        "ACOD1, ADAM8, AIM2",
                        "B2M, CD74, CTSS"),
              Term = c(
              "peptide antigen assembly with MHC class II protein complex",
              "innate immune response",
              "antigen processing and presentation of exogenous
               peptide antigen via MHC class II")
)

wordcloud <- enrichmentWordcloud(geneset_df)


## Example using the data available in the package

data(macrophage_topGO_example,
     package = "GeDi",
     envir = environment())
wordcloud <- enrichmentWordcloud(macrophage_topGO_example)