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

 Package: DEsubs

-Version: 1.0.0

+Version: 1.0.1

 Date: 2015-07-19

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -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 +1,3 @@

-...

\ No newline at end of file

+1.0.1: - All visualization functions now have the appropriate return values.

+

+1.0.0: - Initial version

\ No newline at end of file

@@ -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 

@@ -88,9 +88,9 @@ load(system.file('extdata', 'data.RData', package='DEsubs'))

 \newpage

 ## 2. User Input

-DEsubs accepts RNA-seq expression control-case profile data. The following 

-example in Table 1 shows the right structure for RNA-seq expression data input.

-

+DEsubs accepts RNA-seq expression paired case-control profile data. The 

+following example in Table 1 shows the right structure for RNA-seq expression

+data input.

 ```{r, eval=TRUE, echo=FALSE, results = 'asis'}

@@ -103,7 +103,7 @@ data <- c(    1879, 2734, 2369, 2636, 2188, 9743, 9932, 10099,

 data <- matrix(data, nrow=6, ncol=8, byrow=TRUE)

 rownames(data) <- c(paste0('Gene ', 1:3), '...',  'Gene N-1', 'Gene N')

-colnames(data) <- paste0('Sample ', 1:8)

+colnames(data) <- c(paste0('Case ', 1:4), paste0('Control ', 1:4))

 kable( data,

     caption = 'Example of user input format' )