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

 Package: DEsubs

-Version: 1.6.0

+Version: 1.6.1

 Date: 2017-07-23

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -72,6 +72,10 @@ references.

 load(system.file('extdata', 'data.RData', package='DEsubs'))

+outfile.topological <- tempfile(fileext='.pdf') 

+outfile.functional <- tempfile(fileext='.pdf') 

+outfile.barplot <- tempfile(fileext='.pdf') 

+

 res <- geneVisualization(  

             DEsubs.out=DEsubs.out, top=10,

             measures.topological=c( 'degree', 'betweenness', 'closeness',

@@ -82,6 +86,10 @@ res <- geneVisualization(

             size.topological=c(5,4),

             size.functional=c(7,4),

             size.barplot=c(5,6),

-            export='pdf', verbose=FALSE)

+            export='pdf',

+            outfile.topological=outfile.topological,

+            outfile.functional=outfile.functional,

+            outfile.barplot=outfile.barplot,

+            verbose=FALSE)

 }

@@ -43,10 +43,14 @@ Organism level measures

 load(system.file('extdata', 'data.RData', package='DEsubs'))

+outfile <- tempfile(fileext='.pdf')  

+

 res <- organismVisualization( 

                 DEsubs.out=DEsubs.out, references='KEGG', 

                 topSubs=10, topTerms=20,

-                export='pdf', width=7, height=6,

+                width=7, height=6,

+                export='pdf', 

+                outfile=outfile,

                 verbose=FALSE)

 }

@@ -34,12 +34,14 @@ Subpathway plotting as a graph.

 load(system.file('extdata', 'data.RData', package='DEsubs'))

+outfile <- tempfile(fileext='.pdf')  

 res <- subpathwayToGraph( 

                 DEsubs.out=DEsubs.out, 

                 submethod='community.walktrap', 

                 subname=paste0('sub', 6),

                 size=c(10,10),

-                export='pdf' )

+                export='pdf',

+                outfile=outfile )

 }

@@ -56,12 +56,16 @@ issues.

 load(system.file('extdata', 'data.RData', package='DEsubs'))

+outfile <- tempfile(fileext='.pdf') 

+

 res <- subpathwayVisualization( 

                 DEsubs.out=DEsubs.out,  

                 references=c('TF'), 

                 submethod='community.walktrap',

                 subname='sub1', 

-                scale=c(1.0), export='pdf')

+                scale=c(1.0), 

+                export='pdf',

+                outfile=outfile )

 }

@@ -716,7 +716,7 @@ res <- subpathwayToGraph(

                     DEsubs.out=DEsubs.out, 

                     submethod='community.walktrap', 

                     subname='sub6', verbose=FALSE,

-                    export=c('plot', 'gml', 'edgelist') )

+                    export='plot' )

 ```

@@ -735,7 +735,7 @@ res <- subpathwayToGraph(

                     submethod='community.walktrap', 

                     subname='sub6', 

                     verbose=FALSE,

-                    export=c('plot', 'gml', 'edgelist') )

+                    export='plot' )

 ```

 Subpathway enrichment in association with biological and pharmacological