vignettes and documents update

DESCRIPTION

@@ -1,20 +1,21 @@
 Package: SBGNview
-Title: Overlay omics data onto SBGN pathway diagram
+Title: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
 Description: 
-    SBGNview is a tool set for visualizing omics data on pathway maps and pathway related data analysis.
-    Given an omics data table and a pathway file (SBGN-ML format with layout information), SBGNview 
-    overlays omics data as colors on glyphs (nodes) and output image files.
-    Pathway is rendered with community standard notation: Systems Biology Graphical Notation (SBGN).
-    Currently it maps gene/protein data to “macromolecule” glyphs and maps chemical compound data to “simple chemical” glyphs.
-    For omics data, SBGNview supports common gene/protein/compound ID types (e.g. Entrez Gene ID, UNIPROT, ChEBI etc.).
-    SBGNview can automatically retrieve and use SBGN-ML files from common pathway databases
-    (e.g. Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc.).
-    Extensive options are provided to control glyph and edge features.
-    SBGNview can search for pathways by keywords, extract node information and highlight shortest path between two nodes.  
+   SBGNview is a tool set for pathway based data visalization,
+   integration and analysis. SBGNview is similar and complementary to
+   the widely used Pathview, with the following key features:
+   1. Pathway definition by the widely adopted Systems Biology
+   Graphical Notation (SBGN); 2. Supports multiple major pathway
+   databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP)
+   and user defined pathways; 3. Covers 5,200 reference pathways and
+   over 3,000 species by default; 4. Extensive graphics controls,
+   including glyph and edge attributes, graph layout and sub-pathway
+   highlight; 5. SBGN pathway data manipulation, processing,
+   extraction and analysis.
 Version: 1.5.1
 Author:
-    Xiaoxi Dong, Kovidh Vegesna, Weijun Luo
-Maintainer: Kovidh Vegesna <[email protected]>, Weijun Luo <[email protected]>
+    Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo
+Maintainer: Weijun Luo <[email protected]>
 Depends:
     R (>= 3.6),
     pathview,
@@ -40,16 +41,16 @@ License: AGPL-3
 LazyData: FALSE
 Collate:
     SBGN.to.SVG.R
-    parsing.utilities.R
-    plot.utilities.R
-    data.R
     SBGNview.R
     SBGNview.obj.fun.R
     color.panel.R
+    data.R
+    download.utilities.R
     highlight.utilities.R
-    zzz.R
     mapping.utilities.R
-    download.utilities.R
+    parsing.utilities.R
+    plot.utilities.R
+    zzz.R
 RoxygenNote: 7.1.1
 Suggests:
     testthat,

NEWS

@@ -1,2 +1,11 @@
-Changes before version 0.99.100 (2019-05-15)
-+ Submitting to Bioconductor
+VERSION 1.5.1/1.4.1 (2021-02)
+-------------
+
+  o Massive updates and rewriting of SBGNview, by Kovidh Vegesna and Weijun Luo.
+
+VERSION 0.99.100 (2019-05)
+-------------
+
+  o Initial release of SBGNview, developed by Xiaoxi Dong and Weijun Luo
+
+

README.md

@@ -12,7 +12,7 @@ Key features:
 
 * Pathway diagram and definition by the widely adopted [SBGN standard formats](https://sbgn.github.io/);
 
-* Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
+* Supports multiple major pathway databases beyond KEGG ([Reactome](https://reactome.org/), [MetaCyc](https://metacyc.org/), [SMPDB](https://smpdb.ca/), [PANTHER](http://www.pantherdb.org/pathway/), [METACROP](https://metacrop.ipk-gatersleben.de/) etc) and user defined pathways;
 
 * Covers 5,200 reference pathways and over 3,000 species by default;
 
@@ -27,8 +27,6 @@ Please cite the following papers when using this open-source  package. This will
 Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, <a href=https://doi.org/10.1093/bioinformatics/btt285>doi: 10.1093/bioinformatics/btt285</a>
 
 
-Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020.
-
 ## Installation
 
 ### Prerequisites

vignettes/SBGNview.Vignette.Rmd

@@ -1,6 +1,9 @@
 ---
-title: "SBGNview: data integration, visualization and analysis on SBGN pathways"
-author: "Xiaoxi Dong, Kovidh Vegesna, Weijun Luo"
+title: "SBGNview: Data Analysis, Integration and Visualization on Massive SBGN Pathway Collections"
+author: 
+  - Xiaoxi Dong
+  - Kovidh Vegesna, kvegesna (AT) uncc.edu
+  - Weijun Luo, luo_weijun (AT) yahoo.com
 date:  "`r format(Sys.time(), '%d %B, %Y')`"
 output: 
     bookdown::html_document2:
@@ -25,7 +28,7 @@ SBGNview is a tool set for pathway based data visalization, integration and anal
 
 * Pathway definition by the widely adopted [Systems Biology Graphical Notation (SBGN)](https://sbgn.github.io/);
 
-* Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
+* Supports multiple major pathway databases beyond KEGG ([Reactome](https://reactome.org/), [MetaCyc](https://metacyc.org/), [SMPDB](https://smpdb.ca/), [PANTHER](http://www.pantherdb.org/pathway/), [METACROP](https://metacrop.ipk-gatersleben.de/) etc) and user defined pathways;
 
 * Covers 5,200 reference pathways and over 3,000 species by default;
 
@@ -40,8 +43,6 @@ Please cite the following papers when using this open-source  package. This will
 Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, <a href=https://doi.org/10.1093/bioinformatics/btt285>doi: 10.1093/bioinformatics/btt285</a>
 
 
-Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020.
-
 # Installation and quick start
 Please see the [Quick Start tutorial](https://bioconductor.org/packages/devel/bioc/vignettes/SBGNview/inst/doc/SBGNview.quick.start.html) for installation instructions and quick start examples.
 

vignettes/SBGNview.quick.start.Rmd

@@ -1,6 +1,8 @@
 ---
-title: "SBGNview quick start"
-author: "Weijun Luo, Kovidh Vegesna"
+title: "SBGNview Quick Start"
+author: 
+  - Weijun Luo, luo_weijun (AT) yahoo.com
+  - Kovidh Vegesna, kvegesna (AT) uncc.edu
 date:  "`r format(Sys.time(), '%d %B, %Y')`"
 output: 
     bookdown::html_document2:
@@ -29,7 +31,7 @@ Key features:
 
 * Pathway definition by the widely adopted [Systems Biology Graphical Notation (SBGN)](https://sbgn.github.io/);
 
-* Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
+* Supports multiple major pathway databases beyond KEGG ([Reactome](https://reactome.org/), [MetaCyc](https://metacyc.org/), [SMPDB](https://smpdb.ca/), [PANTHER](http://www.pantherdb.org/pathway/), [METACROP](https://metacrop.ipk-gatersleben.de/) etc) and user defined pathways;
 
 * Covers 5,200 reference pathways and over 3,000 species by default;
 
@@ -44,8 +46,6 @@ Please cite the following papers when using this open-source  package. This will
 Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, <a href=https://doi.org/10.1093/bioinformatics/btt285>doi: 10.1093/bioinformatics/btt285</a>
 
 
-Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020.
-
 # Installation
 
 ## Prerequisites

vignettes/pathway.enrichment.analysis.Rmd

@@ -1,6 +1,9 @@
 ---
-title: "Pathway analysis and visualization using SBGNview collected gene set"
-author: "Xiaoxi Dong, Weijun Luo"
+title: "SBGNview Based Pathway Analysis and Visualization Workflow"
+author: 
+  - Xiaoxi Dong
+  - Kovidh Vegesna, kvegesna (AT) uncc.edu
+  - Weijun Luo, luo_weijun (AT) yahoo.com
 date:  "`r format(Sys.time(), '%d %B, %Y')`"
 output: 
     bookdown::html_document2:
@@ -30,7 +33,6 @@ Please cite the following papers when using the open-source SBGNview package. Th
 
 Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, <a href=https://doi.org/10.1093/bioinformatics/btt285>doi: 10.1093/bioinformatics/btt285</a>
 
-Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020.
 
 
 Please also cite the GAGE paper when using the gage package: