diff --git a/R/pathway_analysis.R b/R/pathway_analysis.R index aa5e545..082a2a8 100644 --- a/R/pathway_analysis.R +++ b/R/pathway_analysis.R @@ -73,7 +73,7 @@ pathway_analysis <- function(x, species = c("human", "mouse")) { keggres <- gage::gage(foldchanges, gsets = kegg.sigmet.gs, same.dir = TRUE) # if plotting then do so here - we plot the top 3 upregulated and downregulated - if (plot { + if (plot) { keggrespathways.up <- data.frame(id = rownames(keggres$greater), keggres$greater) %>% tbl_df() %>% filter(row_number() <= 3) %>%