@@ -1,5 +1,5 @@

 Package: DEsubs

-Version: 1.1.1

+Version: 1.1.2

 Date: 2015-07-19

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -339,7 +339,7 @@ subpathwayVisualization <- function( DEsubs.out,

                                 references='', 

                                 submethod, 

                                 subname,

-                                colors=c('#FF0000FF', '#FF9900FF', '#CCFF00FF',

+                                colors=c('#FF0000FF', '#FF9900FF','#CCFF00FF',

                                         '#33FF00FF', '#00FF66FF', '#0066FFFF',

                                         '#3300FFFF', '#CC00FFFF', '#FF0099FF',

                                         '#EE82EEFF'), 

@@ -371,9 +371,10 @@ subpathwayVisualization <- function( DEsubs.out,

     }

     if ( '' %in% outfiles ) { outfiles <- rep('', length(references) ) }

+    out <- vector(mode='list', length=length(references))

     for ( i in seq_len(length(references)) )

     {

-        .subpathwayVisualization(DEsubs.out=DEsubs.out,

+        out[[i]] <- .subpathwayVisualization(DEsubs.out=DEsubs.out,

                                 reference=references[i],

                                 submethod=submethod,

                                 subname=subname,

@@ -385,6 +386,9 @@ subpathwayVisualization <- function( DEsubs.out,

                                 verbose=verbose

                                 )

     }

+    names(out) <- references

+

+    return( out )

 }

 .subpathwayVisualization <- function( DEsubs.out, reference, submethod, 

@@ -503,9 +507,15 @@ subpathwayVisualization <- function( DEsubs.out,

     adjmat   <- matrix(0, nrow=length(rowTerms), ncol=length(colTerms))

     rownames(adjmat) <- rowTerms

     colnames(adjmat) <- colTerms

+    adjmat.pval <- matrix(NA, nrow=length(rowTerms), ncol=length(colTerms))

+    rownames(adjmat.pval) <- rowTerms

+    colnames(adjmat.pval) <- colTerms    

     for ( i in seq_len(nrow(edgeList)) )

     {

+        # For visualization purposes

         adjmat[ edgeList[i,1], edgeList[i,2] ] <- 1

+        # For output

+        adjmat.pval[edgeList[i,1], edgeList[i,2]] <- as.numeric(edgeList[i,3])

     }

     if ( shuffleColors  )

@@ -538,6 +548,8 @@ subpathwayVisualization <- function( DEsubs.out,

                 export=export)

     if (verbose) { message('done.') }

+

+    return( adjmat.pval )

 }

@@ -571,9 +583,10 @@ organismVisualization <- function( DEsubs.out,

     }

     if ( '' %in% outfiles ) { outfiles <- rep('', length(references) ) }

+    out <- vector(mode='list', length=length(references))

     for ( i in seq_len(length(references)) )

     {

-        res <- .organismVisualization(DEsubs.out=DEsubs.out,

+        out[[i]] <- .organismVisualization(DEsubs.out=DEsubs.out,

                                     references=references[i],

                                     topSubs=topSubs,

                                     topTerms=topTerms,

@@ -584,9 +597,9 @@ organismVisualization <- function( DEsubs.out,

                                     outfile=outfiles[i],

                                     verbose=verbose)

     }

+    names(out) <- references

-

-    return(invisible())

+    return( out )

 }

 .organismVisualization <- function( DEsubs.out, references, topSubs, topTerms,

@@ -712,7 +725,7 @@ organismVisualization <- function( DEsubs.out,

         { message('done', appendLF = TRUE) }

-    return(termsPerSub.edgeList)

+    return( termsPerSub.df )

 }

@@ -1,3 +1,6 @@

-1.1.1: - Update in User Guide/User Input

+1.1.2:  - All visualization functions now return visualized data.

+        - Added support for organism Danio rerio (zebrafish).

-1.1.0: - Initial version

\ No newline at end of file

+1.1.1:  - Update in User Guide/User Input

+

+1.1.0:  - Initial version

\ No newline at end of file

Binary files a/inst/extdata/Data/edgeLists.RData and b/inst/extdata/Data/edgeLists.RData differ

@@ -8,7 +8,8 @@ DEsubs(org, mRNAexpr, mRNAnomenclature, pathways, DEtool, DEpar,

     CORtool, CORpar, subpathwayType, rankedList, verbose)

 }

 \arguments{

-\item{org}{Organism identifier ('hsa', 'mmu', 'rno', 'sce', 'ath', 'dme')}

+\item{org}{Organism identifier ('hsa', 'mmu', 'rno', 'sce', 'ath', 'dme', 

+'dre')}

 \item{mRNAexpr}{RNA-seq expression data in the form of either a matrix

 or a filename of a text file stored in the 'User' directory.}

 \item{mRNAnomenclature}{mRNAnomenclature ('entrezgene', 'ensembl_gene_id',

@@ -31,7 +31,8 @@ not specified, default filenames are used ('DEsubs/Output').}

 \item{verbose}{ TRUE to display informative messages, FALSE to hide. }

 }

 \value{

-No value is returned.

+A list of matrices, containing Subpathway/Term/P-Value results for each

+reference.

 }

 \description{

 Organism level measures

@@ -38,7 +38,9 @@ not specified, default filenames are used ('DEsubs/Output').}

 \item{verbose}{ TRUE to display informative messages, FALSE to hide. }

 }

 \value{

-No value is returned.

+A list of matrices, each containing the  P-Value of enrichment between the 

+terms for a specific reference (rows) and each of the subpathway genes 

+(columns). If there is no enrichment, the value is NA. 

 }

 \description{

 Circular diagrams containing subpathways enrichment in potential key 

@@ -122,8 +122,9 @@ data <- c(  'Homo sapiens', "'hsa'",

             'Drosophila melanogaster', "'dme'", 

             'Saccharomyces cerevisiae', "'sce'",

             'Arabidopsis thaliana', "'ath'",

-            'Rattus norvegicus', "'rno'")

-data <- matrix(data, nrow=6, ncol=2, byrow=TRUE)

+            'Rattus norvegicus', "'rno'",

+            'Danio rerio', "'dre'")

+data <- matrix(data, nrow=7, ncol=2, byrow=TRUE)

 rownames(data) <- rep('', nrow(data))

 colnames(data) <- c('Supported Organisms', 'R command')