better viewPathway and rm site

YuLab-SMU · Mar 15, 2018 · cfff124 · cfff124
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ReactomePA
 Type: Package
 Title: Reactome Pathway Analysis
-Version: 1.23.1
+Version: 1.23.2
 Authors@R: c(person(given = "Guangchuang", family = "Yu",
 	   	    email = "[email protected]",
 		    role  = c("aut", "cre")),
@@ -13,7 +13,7 @@ Description: This package provides functions for pathway analysis based on
     REACTOME pathway database. It implements enrichment analysis, gene set
     enrichment analysis and several functions for visualization.
 Depends:
-    R (>= 3.3.1)
+    R (>= 3.4.0)
 Imports:
     AnnotationDbi,
     DOSE (>= 3.5.1),
@@ -33,7 +33,7 @@ Suggests:
 VignetteBuilder: knitr
 ByteCompile: true
 License: GPL-2
-URL: https://guangchuangyu.github.io/ReactomePA
+URL: https://guangchuangyu.github.io/software/ReactomePA
 BugReports: https://github.com/GuangchuangYu/ReactomePA/issues
 Packaged: 2012-03-05 18:26:53 UTC; mcarlson
 biocViews: Pathways, Visualization, Annotation, MultipleComparison,

diff --git a/NAMESPACE b/NAMESPACE
@@ -29,6 +29,7 @@ importFrom(ggplot2,scale_size)
 importFrom(ggplot2,theme_void)
 importFrom(ggraph,geom_edge_link)
 importFrom(ggraph,geom_node_point)
+importFrom(ggraph,geom_node_text)
 importFrom(ggraph,ggraph)
 importFrom(graphite,convertIdentifiers)
 importFrom(graphite,pathwayGraph)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,12 @@
+CHANGES IN VERSION 1.23.2
+------------------------
+ o re-implement viewPathway <2018-03-15, Thu>
+ o mv site to https://guangchuangyu.github.io/software/ReactomePA
+
+CHANGES IN VERSION 1.23.1
+------------------------
+ o import enrichplot
+
 CHANGES IN VERSION 1.21.3
 ------------------------
  o new project site using blogdown <2017-09-30, Fri>

diff --git a/R/viewPathway.R b/R/viewPathway.R
@@ -13,10 +13,12 @@
 ##' @importFrom graphite pathwayGraph
 ##' @importFrom igraph igraph.from.graphNEL
 ##' @importFrom igraph as.undirected
+##' @importFrom igraph "V<-"
 ##' @importFrom DOSE EXTID2NAME
 ##' @importFrom ggraph ggraph
 ##' @importFrom ggraph geom_edge_link
 ##' @importFrom ggraph geom_node_point
+##' @importFrom ggraph geom_node_text
 ##' @importFrom ggplot2 aes_
 ##' @importFrom ggplot2 scale_color_continuous
 ##' @importFrom ggplot2 scale_size
@@ -81,18 +83,21 @@ viewPathway <- function(pathName,
     gg <- igraph.from.graphNEL(g)
     gg <- as.undirected(gg)
     gg <- setting.graph.attributes(gg)
+    V(gg)$name <- sub("[^:]+:", "", V(gg)$name)
+
     if (!is.null(foldChange)) {
         ## gg <- scaleNodeColor(gg, foldChange)
-        fc <- foldChange[sub("[^:]+:", "", V(gg)$name)]
+        fc <- foldChange[V(gg)$name]
         V(gg)$color <- fc
-        palette <- enrichplot:::fc_palette(fc)
+        ## palette <- enrichplot:::fc_palette(fc)
 
     }
     ## netplot(gg, foldChange=foldChange, ...)
     ggraph(gg, layout=layout) +
         geom_edge_link(alpha=.8, colour='darkgrey') +
         geom_node_point(aes_(color=~as.numeric(as.character(color)), size=~size)) +
-        scale_color_continuous(low="red", high="blue", name = "fold change", na.value = "#E5C494") + 
+        scale_color_continuous(low="red", high="blue", name = "fold change", na.value = "#E5C494") +
+        geom_node_text(aes_(label=~name), repel=TRUE) +
         ## scale_color_gradientn(name = "fold change", colors=palette, na.value = "#E5C494") +
         scale_size(guide = FALSE) + theme_void()
 }

diff --git a/README.Rmd b/README.Rmd
@@ -18,13 +18,12 @@ library("yyplot")
 `r badge_bioc_release("ReactomePA", "green")`
 `r badge_devel("guangchuangyu/ReactomePA", "green")`
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since)
-`r badge_bioc_download("ReactomePA", "total", "blue")`
-`r badge_bioc_download("ReactomePA", "month", "blue")`
+[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
+
 
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![codecov](https://codecov.io/gh/GuangchuangYu/ReactomePA/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ReactomePA/)
 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ReactomePA/commits/master)
-[![commit](http://www.bioconductor.org/shields/commits/bioc/ReactomePA.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source)
 [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/network)
 [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/stargazers)
 
@@ -45,7 +44,10 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
 + [Feedback](https://guangchuangyu.github.io/ReactomePA/#feedback)
 
 
-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ReactomePA.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract)
+[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract)
+`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`
+`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`
+
 
 ------------------------------------------------------------------------
 
@@ -63,16 +65,8 @@ __*G Yu*__, QY He^\*^. ReactomePA: an R/Bioconductor package for reactome pathwa
 
 ### Citation
 
-`r badge_citation("8d8msizDQcsC", "3311691878690959578", "green")`
-
 
-```{r echo=F, comment=NA}
-p <- plot_citation_trend('DO5oG40AAAAJ', '8d8msizDQcsC')
-ggsave(p, file="docs/images/citation.png", width=8, height=4)
-```
-
-
-<img src="docs/images/citation.png" width="890"/>
+<img src="https://guangchuangyu.github.io/software/ReactomePA/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
 
 
 ### Download stats
@@ -82,15 +76,5 @@ ggsave(p, file="docs/images/citation.png", width=8, height=4)
 `r badge_bioc_download("ReactomePA", "month", "blue")`
 
 
-
-```{r echo=F, message=F, comment=NA}
-x <- dlstats::bioc_stats("ReactomePA")
-x <- x[-nrow(x), ] # last month data is not complete
-p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
-    theme_minimal() +xlab(NULL) + ylab(NULL) +
-    labs(title="ReactomePA", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
-ggsave(p, file="docs/images/dlstats.png", width=8, height=4)
-```
-
-<img src="docs/images/dlstats.png" width="890"/>
+<img src="https://guangchuangyu.github.io/software/ReactomePA/index_files/figure-html/unnamed-chunk-2-1.png" width="890"/>
 
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 ReactomePA: Reactome Pathway Analysis
 =====================================
 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.22.0-green.svg?style=flat)](https://bioconductor.org/packages/ReactomePA) [![develVersion](https://img.shields.io/badge/devel%20version-1.23.1-green.svg?style=flat)](https://github.com/guangchuangyu/ReactomePA) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since) [![total](https://img.shields.io/badge/downloads-24923/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA) [![month](https://img.shields.io/badge/downloads-623/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA)
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.22.0-green.svg?style=flat)](https://bioconductor.org/packages/ReactomePA) [![develVersion](https://img.shields.io/badge/devel%20version-1.23.2-green.svg?style=flat)](https://github.com/guangchuangyu/ReactomePA) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ReactomePA/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ReactomePA/) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--06-green.svg)](https://github.com/GuangchuangYu/ReactomePA/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ReactomePA.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/stargazers)
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ReactomePA/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ReactomePA/) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--15-green.svg)](https://github.com/GuangchuangYu/ReactomePA/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ReactomePA.svg)](https://github.com/GuangchuangYu/ReactomePA/stargazers)
 
 [![platform](http://www.bioconductor.org/shields/availability/devel/ReactomePA.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ReactomePA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ReactomePA/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ReactomePA) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ReactomePA/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ReactomePA)
 
@@ -15,7 +15,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
 -   [Featured Articles](https://guangchuangyu.github.io/ReactomePA/featuredArticles/)
 -   [Feedback](https://guangchuangyu.github.io/ReactomePA/#feedback)
 
-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ReactomePA.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract)
+[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
 
 ------------------------------------------------------------------------
 
@@ -29,12 +29,10 @@ Please cite the following article when using `ReactomePA`:
 
 ### Citation
 
-[![citation](https://img.shields.io/badge/cited%20by-59-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=3311691878690959578)
-
-<img src="docs/images/citation.png" width="890"/>
+<img src="https://guangchuangyu.github.io/software/ReactomePA/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
 
 ### Download stats
 
-[![download](http://www.bioconductor.org/shields/downloads/ReactomePA.svg)](https://bioconductor.org/packages/stats/bioc/ReactomePA/) [![total](https://img.shields.io/badge/downloads-24923/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA) [![month](https://img.shields.io/badge/downloads-623/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA)
+[![download](http://www.bioconductor.org/shields/downloads/ReactomePA.svg)](https://bioconductor.org/packages/stats/bioc/ReactomePA/) [![total](https://img.shields.io/badge/downloads-25096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA) [![month](https://img.shields.io/badge/downloads-623/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA)
 
-<img src="docs/images/dlstats.png" width="890"/>
+<img src="https://guangchuangyu.github.io/software/ReactomePA/index_files/figure-html/unnamed-chunk-2-1.png" width="890"/>
diff --git a/docs/categories/index.xml b/docs/categories/index.xml