PCA plots and enrichment tables has been fixed

inst/templates/pca_enr.Rmd

@@ -1,29 +1,29 @@
 ```{r , echo=FALSE, results='asis', message=FALSE, warning=FALSE}
 	print_go_tables <- function(all_enr) {
 		cat("\n\n\n<br>")
-			cat('<div style="display:flex; flex-wrap: wrap;">')
-		for (dimension in names(all_enr)) {
-
-			cat('<div style ="width:50%">')
-			cat(paste0("\n**",dimension,"**<br>"))
-			top_GOs <- head(all_enr[[dimension]], 10)
-			if (nrow(top_GOs) != 0){
-				top_GOs <- top_GOs[,c("GO.ID","Term","p.value","fdr")]
-				top_GOs[,c("p.value","fdr")]<- format(top_GOs[,c("p.value","fdr")], scientific = TRUE, digits = 3)
+		
+		
+		 merged_df <- all_enr |>
+		 purrr::imap(~ rename_fdr_column(.x, .y)) |>
+		 purrr::reduce(dplyr::full_join, by = c("GO.ID", "Term"))
+		 merged_columns <- colnames(merged_df)[!colnames(merged_df) %in% c("GO.ID", "Term")]
+
+				merged_df[,merged_columns]<- format(merged_df[,merged_columns], scientific = TRUE, digits = 3)
 				print(htmltools::tagList(
-					DT::datatable(top_GOs, filter = 'top', rownames = FALSE, extensions = c('Buttons','ColReorder'),
+					DT::datatable(merged_df, filter = 'top', rownames = FALSE, extensions = c('Buttons','ColReorder'),
 		                    options = list(
 		                      colReorder = TRUE,
 		                      dom = 'lftBip',
 		                        buttons = c('copy', 'csv', 'excel')))
 				))
-			} else {
-				cat("\n**No enrichments found**\n")
-			}
-			cat("</div>")
+			
+	}
 
-		}	
-		cat("</div>")
+	rename_fdr_column <- function(df, name) {
+		 df <- df[df$fdr <= 0.05,]
+		 df |>
+		   dplyr::select(GO.ID, Term, fdr) |>
+		   dplyr::rename(!!name := fdr)
 	}
 ```
 ```{r "{{funsys}}_enr", echo=FALSE, results='asis', message=FALSE, warning=FALSE}
@@ -35,18 +35,20 @@ last_dim <- 1
 while (last_dim < func_results$pca_data$all_genes$dim_to_keep){
 	plot(FactoMineR::plot.PCA(func_results$pca_data$all_genes$pca_data, 
 						invisible = "quali", 
-						axis = c(last_dim, last_dim + 1), 
+						axes = c(last_dim, last_dim + 1), 
 						title = paste0(last_dim, " and ", last_dim + 1, " PCs")))
 	last_dim <- last_dim + 2
 } 
 
 print_go_tables(pca_enr_all)
+cat("<br> This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs<br>")
 
 cat("### **Functional enrichments of HCPC clusters using all genes**\n")
 plot(func_results$pca_data$all_genes$res.hcpc, choice="tree", title="")
 plot(func_results$pca_data$all_genes$res.hcpc,  axes=c(1,2), choice="map", draw.tree= FALSE)
 
 print_go_tables(pca_cl_all)
+cat("<br> This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters<br>")
 
 
 cat("### **Functional enrichments of PCs using only DEGs**\n")
@@ -55,12 +57,13 @@ last_dim <- 1
 while (last_dim < func_results$pca_data$DEGs$dim_to_keep){
 	plot(FactoMineR::plot.PCA(func_results$pca_data$DEGs$pca_data, 
 		invisible = "quali", 
-		axis = c(last_dim, last_dim + 1), 
+		axes = c(last_dim, last_dim + 1), 
 		title = paste0(last_dim, " and ", last_dim + 1, " PCs")))
 	last_dim <- last_dim + 2
 } 
 
 print_go_tables(pca_enr_degs)
+cat("<br> This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs<br>")
 
 cat("### **Functional enrichments of HCPC clusters using only DEGs**\n")
 
@@ -69,6 +72,7 @@ plot(func_results$pca_data$DEGs$res.hcpc,  axes=c(1,2), choice="map", draw.tree=
 
 print_go_tables(pca_cl_degs)
 
+cat("<br> This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters<br>")
 
 
 ```