Added feature quality of life in go.R

benjamin-james · benjamin-james · commit 18114c728694 · 2025-06-30T14:37:17.000-04:00
diff --git a/R/go.R b/R/go.R
@@ -53,6 +53,8 @@ enrichALL_Excel <- function(xlsx, new_sheet, OrgDb, method, gene_col="gene",
     if ((meth_path %in% sheet_names)&&(nrow(df)>0)) {
       df$log2FC=min_log2FC
       df$FDR=max_FDR
+      df$mlog10p.adjust <- -log10(df$p.adjust)
+      df$DescID <- paste0(df$Description, " (", df$ID, ")")
       mpdf <- openxlsx::readWorkbook(wb, sheet=meth_path)
       I <- intersect(colnames(mpdf), colnames(df))
       if (length(I) == ncol(df)) {
@@ -68,7 +70,7 @@ enrichALL_Excel <- function(xlsx, new_sheet, OrgDb, method, gene_col="gene",
       }
     }
     if (nrow(df) > 0) {
-      openxlsx::writeData(wb, meth_path, df)
+      openxlsx::writeData(wb, meth_path, df, withFilter=TRUE)
     }
     openxlsx::saveWorkbook(wb, xlsx, overwrite=TRUE)
 }

Original file line number	Diff line number	Diff line change
`@@ -53,6 +53,8 @@ enrichALL_Excel <- function(xlsx, new_sheet, OrgDb, method, gene_col="gene",`
`53`	`53`	`if ((meth_path %in% sheet_names)&&(nrow(df)>0)) {`
`54`	`54`	`df$log2FC=min_log2FC`
`55`	`55`	`df$FDR=max_FDR`
	`56`	`+ df$mlog10p.adjust <- -log10(df$p.adjust)`
	`57`	`+ df$DescID <- paste0(df$Description, " (", df$ID, ")")`
`56`	`58`	`mpdf <- openxlsx::readWorkbook(wb, sheet=meth_path)`
`57`	`59`	`I <- intersect(colnames(mpdf), colnames(df))`
`58`	`60`	`if (length(I) == ncol(df)) {`
`@@ -68,7 +70,7 @@ enrichALL_Excel <- function(xlsx, new_sheet, OrgDb, method, gene_col="gene",`
`68`	`70`	`}`
`69`	`71`	`}`
`70`	`72`	`if (nrow(df) > 0) {`
`71`		`- openxlsx::writeData(wb, meth_path, df)`
	`73`	`+ openxlsx::writeData(wb, meth_path, df, withFilter=TRUE)`
`72`	`74`	`}`
`73`	`75`	`openxlsx::saveWorkbook(wb, xlsx, overwrite=TRUE)`
`74`	`76`	`}`