git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DEsubs@128339 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -75,7 +75,7 @@ load(system.file('extdata', 'data.RData', package='DEsubs')) |
75 | 75 |
res <- geneVisualization( |
76 | 76 |
DEsubs.out=DEsubs.out, top=10, |
77 | 77 |
measures.topological=c( 'degree', 'betweenness', 'closeness', |
78 |
- 'hub_score', 'eccentricity', 'page_rank'), |
|
78 |
+ 'eccentricity', 'page_rank'), |
|
79 | 79 |
measures.functional=c( 'KEGG', |
80 | 80 |
'Disease_OMIM', 'Disease_GAD', |
81 | 81 |
'Drug_DrugBank','miRNA', 'TF'), |
... | ... |
@@ -694,7 +694,7 @@ The total picture of the enriched subpathways is performed with dot plots. |
694 | 694 |
res <- geneVisualization( |
695 | 695 |
DEsubs.out=DEsubs.out, top=10, |
696 | 696 |
measures.topological=c( 'degree', 'betweenness', 'closeness', |
697 |
- 'hub_score', 'eccentricity', 'page_rank'), |
|
697 |
+ 'eccentricity', 'page_rank'), |
|
698 | 698 |
measures.functional=c( 'KEGG', 'GO_bp','GO_cc', 'GO_mf', |
699 | 699 |
'Disease_OMIM', 'Disease_GAD', |
700 | 700 |
'Drug_DrugBank','miRNA', 'TF'), |
... | ... |
@@ -750,7 +750,7 @@ res <- geneVisualization( |
750 | 750 |
DEsubs.out=DEsubs.out, |
751 | 751 |
top=12, |
752 | 752 |
measures.topological=c( 'degree', 'betweenness', 'closeness', |
753 |
- 'hub_score', 'eccentricity', 'page_rank'), |
|
753 |
+ 'eccentricity', 'page_rank'), |
|
754 | 754 |
measures.functional=NULL, |
755 | 755 |
measures.barplot=FALSE, |
756 | 756 |
size.topological=c(5,4), |