All significant dimensions are plotted and double are formatted to sc…

…ientifics
seoanezonjic · Jul 29, 2024 · c609d79 · c609d79
1 parent 0594244
commit c609d79
Showing 1 changed file with 20 additions and 19 deletions.
diff --git a/inst/templates/pca_enr.Rmd b/inst/templates/pca_enr.Rmd
@@ -9,6 +9,7 @@
 			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)
 				print(htmltools::tagList(
 					DT::datatable(top_GOs, filter = 'top', rownames = FALSE, extensions = c('Buttons','ColReorder'),
 		                    options = list(
@@ -30,29 +31,29 @@ cat("\n## **{{funsys}} - Enrichments for Principal Components**\n")
 
 cat("### **Functional enrichments of PCs using all genes**\n")
 
-FactoMineR::plot.PCA(func_results$pca_data$all_genes$pca_data, invisible = "quali" , title = "")
+last_dim <- 1
+while (last_dim < func_results$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), 
+						title = paste0(last_dim, " and ", last_dim + 1, " PCs")))
+	last_dim <- last_dim + 2
+} 
 
 print_go_tables(pca_enr_all)
 
 cat("### **Functional enrichments of PCs using only DEGs**\n")
-FactoMineR::plot.PCA(func_results$pca_data$DEGs$pca_data, invisible = "quali" , title = "")
+
+last_dim <- 1
+while (last_dim < func_results$pca_data$all_genes$dim_to_keep){
+	plot(FactoMineR::plot.PCA(func_results$pca_data$DEGs$pca_data, 
+		invisible = "quali", 
+		axis = 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)
 
-# for (dimension in names(pca_enr_degs)) {
-# 	cat(paste0("\n**",dimension,"**\n"))
-# 	top_GOs <- head(pca_enr_degs[[dimension]], 10)
-# 	if (nrow(top_GOs) != 0){
-# 		top_GOs <- top_GOs[,c("GO.ID","Term","p.value","fdr")]
-# 		print(htmltools::tagList(
-# 			DT::datatable(top_GOs, 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")
-# 	}
-# }	
-# pca_enr_degs
+
 ```