Merge pull request #61 from huerqiang/readable

Enable `setReadable` for compareCluster(GSEA algorithm) result
YuLab-SMU · Dec 14, 2021 · 5ce906f · 5ce906f
2 parents 751ca5f + 0521e74
commit 5ce906f
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Showing 4 changed files with 29 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.21.1.9001
+Version: 3.21.1.9002
 Authors@R: c( person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role = c("aut", "cre")),
               person(given = "Li-Gen",      family = "Wang",      email = "[email protected]",   role = "ctb"),
               person(given = "Vladislav",   family = "Petyuk",    email = "[email protected]",          role = "ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
-# DOSE 3.21.1.9001
+# DOSE 3.21.1.9002
 
++ enable `setReadable` for compareCluster(GSEA algorithm) result(2021-12-13, Mon)
 + update the default order of GSEA result (2021-12-09, Thu)
   - if p.adjust is identical, sorted by `abs(NES)`
 

diff --git a/R/accessor.R b/R/accessor.R
@@ -58,14 +58,23 @@ geneInCategory.compareClusterResult <- function(x) {
     ## return(list_new)
 
 
-
-    reslist <- split(x@compareClusterResult, x@compareClusterResult$Cluster)
-
-    res <- lapply(reslist, function(y)
-        setNames(
-            strsplit(y$geneID, split="/", fixed=TRUE),
-            y$ID
-        ))
+    x <- as.data.frame(x)
+    # reslist <- split(x@compareClusterResult, x@compareClusterResult$Cluster)
+    reslist <- split(x, x$Cluster)
+    if ("core_enrichment" %in% colnames(x)) {
+        res <- lapply(reslist, function(y)
+            setNames(
+                strsplit(y$core_enrichment, split="/", fixed=TRUE),
+                y$ID
+            ))
+    } else {
+        res <- lapply(reslist, function(y)
+            setNames(
+                strsplit(y$geneID, split="/", fixed=TRUE),
+                y$ID
+            ))
+    }
+
     res[vapply(res, length, numeric(1)) != 0]
 }
 

diff --git a/R/setReadable.R b/R/setReadable.R
@@ -39,7 +39,13 @@ setReadable <- function(x, OrgDb, keyType="auto") {
     if (isGSEA) {
         genes <- names(x@geneList)
     } else if (isCompare) {
-        genes <- unique(unlist(x@geneClusters))
+        if ("core_enrichment" %in% colnames(as.data.frame(x))) {
+            geneslist <- x@geneClusters
+            names(geneslist) <- NULL
+            genes <- unique(names(unlist(geneslist)))
+        } else {
+            genes <- unique(unlist(x@geneClusters))
+        }     
     } else {
         genes <- x@gene
     }
@@ -73,7 +79,8 @@ setReadable <- function(x, OrgDb, keyType="auto") {
 
 
     geneID <- sapply(gc, paste0, collapse="/")
-    if (isGSEA) {
+    # if (isGSEA) {
+    if ("core_enrichment" %in% colnames(as.data.frame(x))) {
         res$core_enrichment <- unlist(geneID)
     } else {
         res$geneID <- unlist(geneID)