facet with compareCluster result

YuLab-SMU · Nov 3, 2015 · a8fe7b9 · a8fe7b9
1 parent 35ddb9a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clusterProfiler
 Type: Package
 Title: statistical analysis and visulization of functional profiles for
     genes and gene clusters
-Version: 2.5.1
+Version: 2.5.2
 Authors@R: c(person(given = "Guangchuang", family = "Yu",
 	            email = "guangchuangyu@gmail.com",
 		    role  = c("aut", "cre")),
@@ -13,7 +13,7 @@ Authors@R: c(person(given = "Guangchuang", family = "Yu",
 	            email = "giovanni.dallolio@upf.edu",
 		    role = "ctb"))
 Author: Guangchuang Yu <guangchuangyu@gmail.com> with contributions from
-	Li-Gen Wang and Giovanni Dall'Olio.
+    Li-Gen Wang and Giovanni Dall'Olio.
 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
 Description: This package implements methods to analyze and visualize
     functional profiles (GO and KEGG) of gene and gene clusters.
@@ -23,7 +23,7 @@ Imports:
     DOSE,
     GOSemSim,
     AnnotationDbi,
-    methods,	
+    methods,
     stats4,
     tidyr,
     plyr,
@@ -40,13 +40,14 @@ Suggests:
     KEGG.db,
     knitr,
     org.Hs.eg.db,
-    pathview,    
+    pathview,
     ReactomePA,
     RDAVIDWebService
 VignetteBuilder: knitr
 License: Artistic-2.0
 URL: https://github.com/GuangchuangYu/clusterProfiler
 BugReports: https://github.com/GuangchuangYu/clusterProfiler/issues
 Packaged: NA
-biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG, MultipleComparison, Pathways, Reactome, Visualization
-
+biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG,
+    MultipleComparison, Pathways, Reactome, Visualization
+RoxygenNote: 5.0.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(ALLEXTID,BP)
 S3method(ALLEXTID,CC)
@@ -88,6 +88,7 @@ importFrom(KEGGREST,keggLink)
 importFrom(KEGGREST,keggList)
 importFrom(ggplot2,"%+%")
 importFrom(ggplot2,aes)
+importFrom(ggplot2,aes_)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_text)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 2.5.2
+------------------------
+ o facet with compareCluster result <2015-11-03, Tue>
+   + see https://github.com/GuangchuangYu/clusterProfiler/issues/32
+
 CHANGES IN VERSION 2.5.1
 ------------------------
  o read.gmt function for parsing gmt file for enricher and GSEA <2015-10-28, Wed>

diff --git a/R/compareCluster.R b/R/compareCluster.R
@@ -65,9 +65,21 @@ compareCluster <- function(geneClusters, fun="enrichGO", data='', ...) {
         stop("No enrichment found in any of gene cluster, please check your input...")
     }
 
-    clProf.df <- rename(clProf.df, c(.id="Cluster"))
+    clProf.df <- rename(clProf.df, c(.id="Cluster"))    
     clProf.df$Cluster = factor(clProf.df$Cluster, levels=clusters.levels)
 
+    if (is.data.frame(data) && grepl('+', grouping.formula)) {
+        groupVarName <- strsplit(grouping.formula, split="\\+") %>% unlist %>%
+            gsub("~", "", .) %>% gsub("^\\s*", "", .) %>% gsub("\\s*$", "", .)
+        groupVars <- sapply(as.character(clProf.df$Cluster), strsplit, split="\\.") %>% do.call(rbind, .)
+        for (i in seq_along(groupVarName)) {
+            clProf.df[, groupVarName[i]] <- groupVars[,i] 
+        }
+        i <- which(colnames(clProf.df) %in% groupVarName)
+        j <- (1:ncol(clProf.df))[-c(1, i)]
+        clProf.df <- clProf.df[, c(1, i, j)]
+    }
+
     ##colnames(clProf.df)[1] <- "Cluster"
     new("compareClusterResult",
         compareClusterResult = clProf.df,
@@ -182,6 +194,7 @@ setMethod("plot", signature(x="compareClusterResult"),
 ##' @rdname dotplot-methods
 ##' @aliases dotplot,compareClusterResult,ANY-method
 ##' @param object compareClusterResult object
+##' @param x x variable
 ##' @param colorBy one of pvalue or p.adjust
 ##' @param showCategory category numbers
 ##' @param by one of geneRatio, Percentage or count
@@ -192,14 +205,15 @@ setMethod("plot", signature(x="compareClusterResult"),
 ##' @exportMethod dotplot
 setMethod("dotplot", signature(object="compareClusterResult"),
           function(object,
+                   x = ~Cluster,
                    colorBy="p.adjust",
                    showCategory=5,
                    by="geneRatio",
                    includeAll=TRUE,
                    font.size=12,
                    title=""
                    ) {
-              dotplot.compareClusterResult(object, colorBy, showCategory, by, includeAll, font.size, title)
+              dotplot.compareClusterResult(object, x=x, colorBy, showCategory, by, includeAll, font.size, title)
           })
 
 

diff --git a/R/dotplot.R b/R/dotplot.R
@@ -1,6 +1,6 @@
-dotplot.compareClusterResult <- function(object, colorBy="p.adjust", showCategory=5, by="geneRatio", includeAll=TRUE, font.size=12, title="") {
+dotplot.compareClusterResult <- function(object, x=~Cluster, colorBy="p.adjust", showCategory=5, by="geneRatio", includeAll=TRUE, font.size=12, title="") {
     df <- fortify(object, showCategory=showCategory, by=by, includeAll=includeAll)
-    plotting.clusterProfile(df, type="dot", colorBy=colorBy, by=by, title=title, font.size=font.size)
+    plotting.clusterProfile(df, x=x, type="dot", colorBy=colorBy, by=by, title=title, font.size=font.size)
 }
 
 ##' @title fortify
@@ -51,7 +51,7 @@ fortify.compareClusterResult <- function(model, data, showCategory=5, by="geneRa
 
     ## remove zero count
     result$Description <- as.character(result$Description) ## un-factor
-    GOlevel <- result[,c(2,3)] ## GO ID and Term
+    GOlevel <- result[,c("ID", "Description")] ## GO ID and Term
     GOlevel <- unique(GOlevel)
 
     result <- result[result$Count != 0, ]

diff --git a/R/utilities.R b/R/utilities.R
@@ -333,6 +333,7 @@ getGOLevel <- function(ont, level) {
 ##' @return ggplot object
 ##' @importFrom ggplot2 ggplot
 ##' @importFrom ggplot2 aes
+##' @importFrom ggplot2 aes_
 ##' @importFrom ggplot2 aes_string
 ##' @importFrom ggplot2 geom_bar
 ##' @importFrom ggplot2 coord_flip
@@ -348,6 +349,7 @@ getGOLevel <- function(ont, level) {
 ##' @importFrom DOSE theme_dose
 ##' @author Guangchuang Yu \url{http://ygc.name}
 plotting.clusterProfile <- function(clProf.reshape.df,
+                                    x = ~Cluster,
                                     type = "dot",
                                     colorBy = "p.adjust",
                                     by = "geneRatio",
@@ -371,13 +373,13 @@ plotting.clusterProfile <- function(clProf.reshape.df,
     if (type == "dot") {
         if (by == "rowPercentage") {
             p <- ggplot(clProf.reshape.df,
-                        aes(x = Cluster, y = Description, size = Percentage))
+                        aes_(x = x, y = ~Description, size = ~Percentage))
         } else if (by == "count") {
             p <- ggplot(clProf.reshape.df,
-                        aes(x = Cluster, y = Description, size = Count))
+                        aes_(x = x, y = ~Description, size = ~Count))
         } else if (by == "geneRatio") {
             p <- ggplot(clProf.reshape.df,
-                        aes(x = Cluster, y = Description, size = GeneRatio))
+                        aes_(x = x, y = ~Description, size = ~GeneRatio))
         } else {
             ## nothing here
         }

diff --git a/man/DataSet.Rd b/man/DataSet.Rd
diff --git a/man/GSEA.Rd b/man/GSEA.Rd
diff --git a/man/Gff2GeneTable.Rd b/man/Gff2GeneTable.Rd
diff --git a/man/bitr.Rd b/man/bitr.Rd
diff --git a/man/buildGOmap.Rd b/man/buildGOmap.Rd
diff --git a/man/buildKEGGmap.Rd b/man/buildKEGGmap.Rd
diff --git a/man/clusterProfiler-package.Rd b/man/clusterProfiler-package.Rd
diff --git a/man/cnetplot.Rd b/man/cnetplot.Rd
diff --git a/man/compareCluster.Rd b/man/compareCluster.Rd
diff --git a/man/compareClusterResult-class.Rd b/man/compareClusterResult-class.Rd
diff --git a/man/dotplot-methods.Rd b/man/dotplot-methods.Rd
diff --git a/man/download.KEGG.Rd b/man/download.KEGG.Rd
diff --git a/man/dropGO.Rd b/man/dropGO.Rd
diff --git a/man/enrichDAVID.Rd b/man/enrichDAVID.Rd
diff --git a/man/enrichGO.Rd b/man/enrichGO.Rd
diff --git a/man/enrichKEGG.Rd b/man/enrichKEGG.Rd
diff --git a/man/enrichMap.Rd b/man/enrichMap.Rd
diff --git a/man/enricher.Rd b/man/enricher.Rd
diff --git a/man/fortify.compareClusterResult.Rd b/man/fortify.compareClusterResult.Rd
diff --git a/man/getGOLevel.Rd b/man/getGOLevel.Rd
diff --git a/man/gofilter.Rd b/man/gofilter.Rd
diff --git a/man/groupGO.Rd b/man/groupGO.Rd
diff --git a/man/groupGOResult-class.Rd b/man/groupGOResult-class.Rd
diff --git a/man/gseGO.Rd b/man/gseGO.Rd
diff --git a/man/gseKEGG.Rd b/man/gseKEGG.Rd
diff --git a/man/gseaplot.Rd b/man/gseaplot.Rd
diff --git a/man/idType.Rd b/man/idType.Rd
diff --git a/man/merge_result.Rd b/man/merge_result.Rd