Intersect top N enrichment terms per normalization method

Usage

plot_intersection_enrichment(
  se,
  de_res,
  ain = NULL,
  comparisons = NULL,
  id_column = "Gene.Names",
  organism = "hsapiens",
  per_comparison = TRUE,
  sources = c("GO:BP", "GO:MF", "GO:CC"),
  top = 10
)

Arguments

se: SummarizedExperiment containing all necessary information of the proteomics data set
de_res: data table resulting of run_DE
ain: Vector of strings of normalization methods to visualize (must be valid normalization methods saved in de_res)
comparisons: Vector of comparisons (must be valid comparisons saved in de_res)
id_column: String specifying the column of the rowData of the SummarizedExperiment object which includes the gene names
organism: Organism name (gprofiler parameter)
per_comparison: Boolean specifying whether the enrichment analysis should be performed per comparison (TRUE) or on all given comparisons together (FALSE)
sources: Vector of data sources to use (gprofiler parameter)
top: Number of enrichment terms to extract for each normalization method

Value

list of ggplot objects or single ggplot object

Examples

data(tuberculosis_TMT_se)
data(tuberculosis_TMT_de_res)
plot_intersection_enrichment(tuberculosis_TMT_se, tuberculosis_TMT_de_res,
                ain = c("IRS_on_RobNorm", "IRS_on_Median"),
                comparisons = NULL, id_column = "Gene.Names",
                organism = "hsapiens", per_comparison = TRUE,
                sources = c("GO:BP", "GO:MF", "GO:CC"), top = 10)
#> All comparisons of de_res will be visualized.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> Warning: The dcast generic in data.table has been passed a grouped_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(top_go). In the next version, this warning will become an error.
#> $`PTB-HC`

#> 
#> $`TBL-HC`

#> 
#> $`Rx-HC`

#> 
#> $`TBL-PTB`

#> 
#> $`Rx-PTB`

#> 
#> $`Rx-TBL`

#>