From a75322187d1dc9d7c25f0d3c2f7e56bf11282955 Mon Sep 17 00:00:00 2001 From: Weijun Luo Date: Thu, 25 Feb 2021 14:46:36 -0500 Subject: [PATCH] vignettes and documents update --- DESCRIPTION | 37 ++++++++++++----------- NEWS | 13 ++++++-- README.md | 4 +-- vignettes/SBGNview.Vignette.Rmd | 11 ++++--- vignettes/SBGNview.quick.start.Rmd | 10 +++--- vignettes/pathway.enrichment.analysis.Rmd | 8 +++-- 6 files changed, 47 insertions(+), 36 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7526275..3b02283 100644 --- a/DESCRIPTION +++ b/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 , Weijun Luo + Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo +Maintainer: Weijun Luo 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, diff --git a/NEWS b/NEWS index 9607a8e..4075782 100644 --- a/NEWS +++ b/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 + + \ No newline at end of file diff --git a/README.md b/README.md index 6befa1c..e8cbada 100644 --- a/README.md +++ b/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, doi: 10.1093/bioinformatics/btt285 -Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020. - ## Installation ### Prerequisites diff --git a/vignettes/SBGNview.Vignette.Rmd b/vignettes/SBGNview.Vignette.Rmd index c51b27f..bb8de16 100644 --- a/vignettes/SBGNview.Vignette.Rmd +++ b/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, doi: 10.1093/bioinformatics/btt285 -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. diff --git a/vignettes/SBGNview.quick.start.Rmd b/vignettes/SBGNview.quick.start.Rmd index 8a7f37b..50de845 100644 --- a/vignettes/SBGNview.quick.start.Rmd +++ b/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, doi: 10.1093/bioinformatics/btt285 -Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020. - # Installation ## Prerequisites diff --git a/vignettes/pathway.enrichment.analysis.Rmd b/vignettes/pathway.enrichment.analysis.Rmd index 51d0a27..aa72a60 100644 --- a/vignettes/pathway.enrichment.analysis.Rmd +++ b/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, doi: 10.1093/bioinformatics/btt285 -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: