Merge branch 'master' of https://github.com/datapplab/SBGNview_2

README.md

@@ -1,25 +1,38 @@
 
 # SBGNview 
-SBGNview is a tool set for visualizing omics data on SBGN pathway maps.  Given omics data and a SBGN-ML file with layout information, SBGNview can display omics data as colors on glyphs and output image files. SBGNview provides extensive options to control glyph and edge features  (e.g. color, line width etc.). To facilitate pathway based analysis, SBGNview also provides functions to extract glyph information and pairwise interactions from SBGN-ML files. SBGNview can map a large collection of gene, protein and compound ID typs to glyphs.  
 
+[![](https://img.shields.io/badge/release%20version-1.4.1-blue.svg)](https://www.bioconductor.org/packages/SBGNview)
+[![](https://img.shields.io/badge/devel%20version-1.5.1-green.svg)](https://github.com/datapplab/SBGNview)
 
-# Introduction
-Molecular pathways have been widely used in omics data analysis. We previously developed an R/BioConductor package called Pathview, which maps, integrates and visualizes omics data onto KEGG pathway graphs. Since its publication, Pathview has been widely used in numerous omics studies and analysis tools. Here we introduce the SBGNview package, which adopts Systems Biology Graphical Notation (SBGN)[@le2009systems] and greatly extends the Pathview project by supporting multiple major pathway databases besides KEGG.
+
+## Overview
+We previously developed an R/BioConductor package called [Pathview](https://www.bioconductor.org/packages/pathview), which maps, integrates and visualizes a wide range of data onto KEGG pathway graphs. Since its publication, Pathview has been widely used in omics studies and data analyses and has become the leading tool in its category. Here we introduce the SBGNview package, which adopts [Systems Biology Graphical Notation (SBGN)](https://sbgn.github.io/) and greatly extends the Pathview project by supporting multiple major pathway databases beyond KEGG.
 
 Key features:
 
-* Pathway diagram is drawn with SBGN notations 
+* Pathway diagram and definition by SBGN standard formats;
+
+* Supports multiple major pathway databases beyond KEGG and user defined pathways;
+
+* Covers 5,200 reference pathways and over 3,000 species by default;
+
+* Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight;
+
+* SBGN pathway data manipulation, processing, extraction and analysis.
 
-* Supports major pathway databases and user defined pathways. 
+## Citation
 
-* Extensive choices for graphical control. 
+Please cite the following papers when using this open-source  package. This will help the project and our team:
 
-* Pathway related data extraction and analysis
+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>
 
-# Installation
 
-## Prerequisites
-*SBGNview* depends or imports from the following R packages. Note these dependencies will be automatically installed when SBGNview is installed from BioConductor or GitHub
+Dong X, Vegesna K, Luo W. SBGNview: SBGN for pathway based data analysis, integration and visualization, Submitted, 2020.
+
+## Installation
+
+### Prerequisites
+*SBGNview* depends or imports from the following R packages:
 
 * xml2: parse SBGN-ML files
 * rsvg: convert svg files to other formats (pdf, png, ps). librsvg2 is needed to install rsvg. See this page for more details: https://github.com/jeroen/rsvg
@@ -28,9 +41,11 @@ Key features:
 * KEGGREST: generate mapping tables from scratch when needed
 * [pathview](https://bioconductor.org/packages/release/bioc/html/pathview.html): map between different ID types for gene and chemical compound
 * [gage](https://bioconductor.org/packages/release/bioc/html/gage.html): R package for pathway enrichment analysis.
-* [SBGNview.data](https://bioconductor.org/packages/release/data/experiment/html/SBGNview.data.html): demo gene expression datasets for SBGNview package
-* [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html): main function accepts data as SummarizedExperiment objects
-* AnnotationDbi: filter and select data for mapping between IDs
+* [SBGNview.data](https://bioconductor.org/packages/release/data/experiment/html/SBGNview.data.html): demo and supportive datasets for SBGNview package
+* [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html): alternative input user data as SummarizedExperiment objects
+* AnnotationDbi: BioConductor annotation data and infrastructure
+
+Note these dependencies will be automatically installed when SBGNview is installed from BioConductor or GitHub. To install them manually within R:
 
 ```{r setup, eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)){
@@ -39,20 +54,20 @@ if (!requireNamespace("BiocManager", quietly = TRUE)){
 BiocManager::install(c("xml2", "rsvg", "igraph", "httr", "KEGGREST", "pathview", "gage", "SBGNview.data", "SummarizedExperiment", "AnnotationDbi"))
 ```
 
-Dependencies for Operating Systems:  
+External dependencies (outside R):
 **Windows 10**: none
 
 **Linux (Ubuntu)**: needs additional packages (libxml2-dev, libssl-dev, libcurl4-openssl-dev, librsvg2-dev) to be installed. Run the command below in a terminal to install the necessary packages. The same or similar packages can be found for other distributes of linux.
 ```{r depend, eval = FALSE}
 sudo apt install libxml2-dev libssl-dev libcurl4-openssl-dev librsvg2-dev
 ```
 
-## Install SBGNview
-Install **SBGNview** through Bioconductor: 
+### Install SBGNview
+Install SBGNview through Bioconductor: 
 ```{r install, eval = FALSE}
 BiocManager::install(c("SBGNview"))
 ```
-Install **SBGNview** through GitHub:
+Install SBGNview through GitHub:
 ```{r install.1, eval = FALSE}
 install.packages("devtools")
 devtools::install_github("datapplab/SBGNview")
@@ -65,9 +80,9 @@ git clone https://github.com/datapplab/SBGNview.git
 
 ## Quick example
 ```{r, echo = TRUE, eval = TRUE, results = 'hide', message = FALSE, warning = FALSE}
-# load demo dataset and pathway information of built-in collection of SBGN-ML files
 library(SBGNview)
-data("gse16873.d","pathways.info")
+# load demo dataset, SBGN pathway data collection and info, which may take a few seconds
+data("gse16873.d","pathways.info", "sbgn.xmls")
 input.pathways <- findPathways("Adrenaline and noradrenaline biosynthesis")
 SBGNview.obj <- SBGNview(
           gene.data = gse16873.d[,1:3], 
@@ -78,15 +93,10 @@ SBGNview.obj <- SBGNview(
           ) 
 print(SBGNview.obj)
 ```
-Two image files (a .svg file by default and a .png file) will be created in the current working directory.
+Two image files (a svg file by default and a png file) will be created in the current working directory.
 <img src="inst/app/www/quick.start_P00001.svg">   
 
-# Additional information
+## Additional information
 SBGN website: https://sbgn.github.io/
 
-For any questions, please contact Xiaoxi Dong(<[email protected]>) or Weijun Luo(<[email protected]>)
-
-# Citation
-Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir et al. The Systems Biology Graphical Notation Nature Biotechnology, 27(8):735-741, 2009
-
-Luo, Weijun, and Cory Brouwer. "Pathview: an R/Bioconductor package for pathway-based data integration and visualization." Bioinformatics 29.14 (2013): 1830-1831.
+For any questions, please contact Kovidh Vegesna (kvegesna [AT] uncc.edu) or Weijun Luo (luo_weijun [AT] yahoo.com)