Merge branch 'master' of https://github.com/raivokolde/GOsummaries

Conflicts:
	DESCRIPTION

.gitignore

@@ -29,3 +29,5 @@ R/.DS_Store
 *.toc
 
 *.pdf
+
+data/.Rhistory

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: GOsummaries
-Version: 2.0.1
+Version: 2.1.1
 Date: 2014-09-29
 License: GPL (>= 2)
 Description: A package to visualise Gene Ontology (GO) enrichment analysis

NEWS

@@ -1,26 +1,38 @@
-Version 1.99.3
--------------------------------------------------------------------------------
-* Bumped the version number to 1.99.3
+CHANGES IN VERSION 1.99.3
+-------------------------
 
-Version 0.99.3 
--------------------------------------------------------------------------------
-* Updated Vignette to biocStyle
-* Form now GOsummaries is going to live in Bioconductor and this version supersedes the CRAN version 1.1
+CHANGES
 
-Version 0.99.2 
--------------------------------------------------------------------------------
-* Reformatted code for Bioconductor 
-* Improved Vignette
+    o Bumped the version number to 1.99.3
 
+CHANGES IN VERSION 0.99.3 
+--------------------------
 
-Version 1.1
--------------------------------------------------------------------------------
-* Added support for custom data in word clouds (see gosummaries functions)
-* Now it is possible to display genes instead of GO categories (see show_genes parameter in gosummaries.MArrayLM, gosummaries.prcomp and gosummaries.matrix)
-* Added function gosummaries.matrix that takes in a matrix that is a MDS representation of data and expression matrix and then finds most correlated features for each MDS component.	
+NEW FEATURES
 
-Version 1.0
--------------------------------------------------------------------------------
-First version of the package
+    o Updated Vignette to biocStyle
+    o Form now GOsummaries is going to live in Bioconductor and this version supersedes the CRAN version 1.1
 
+CHANGES IN VERSION 0.99.2 
+--------------------------
+
+NEW FEATURES
+
+    o Reformatted code for Bioconductor 
+    o Improved Vignette
+
+
+CHANGES IN VERSION 1.1
+----------------------
+
+    o Added support for custom data in word clouds (see gosummaries functions)
+    o Now it is possible to display genes instead of GO categories (see show_genes parameter in gosummaries.MArrayLM, gosummaries.prcomp and gosummaries.matrix)
+    o Added function gosummaries.matrix that takes in a matrix that is a MDS representation of data and expression matrix and then finds most correlated features for each MDS component.	
+
+CHANGES IN VERSION 1.0
+----------------------
+
+NEW FEATURES
+
+    o First version of the package
 

data/.Rhistory

@@ -1,23 +0,0 @@
-load("/Users/Kolde/Raivo/Projects/GOsummaries/GOsummaries/data/lukk_small.RData")
-load("/Users/Kolde/Raivo/Projects/GOsummaries/Data/testlukk.RData")
-sl
-ls()
-ehad(testlukk)
-str(testlukk)
-str(lukk_small)
-library(plyr)
-data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue))
-daply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6))
-daply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, sample(5:6, 1)))
-dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6))
-unlist(dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6)))
-e = lukk_small$exp[]
-i = unlist(dlply(data.frame(t = lukk_small$annot$Tissue, r = 1:length(lukk_small$annot$Tissue)), "t", function(x) sample(x$r, 6)))
-e = lukk_small$exp[i, ]
-a = lukk_small$annot[i, ]
-e = lukk_small$exp[, i]
-dim(e)
-dim(a)
-tissue_example = list(exp = e, annot = a)
-save(tissue_exampe, file = "~/Raivo/Projects/GOsummaries/GOsummaries/data/tissue_examples.RData")
-save(tissue_example, file = "~/Raivo/Projects/GOsummaries/GOsummaries/data/tissue_examples.RData")