Bumped to v0.0.6. Fixes #1 and #2 by requiring the newer version of k…

…nitr, rmarkdown and knitrBootstrap. Update citations by including rmarkdown. Fix some wording

DESCRIPTION

@@ -2,12 +2,19 @@ Package: derfinderReport
 Type: Package
 Title: Generate HTML reports for derfinder
     (https://github.com/lcolladotor/derfinder) results
-Version: 0.0.5
-Date: 2014-03-30
+Version: 0.0.6
+Date: 2014-04-03
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "lcollado@jhsph.edu"), person("Andrew", "Jaffe", role = "aut", email =
     "andrew.jaffe@libd.org"), person("Jeffrey", "Leek", role = c("aut", "ths"),
     email = "jtleek@gmail.com"))
+Description: Generate HTML reports for results from fast differential
+    expression analysis of RNA-seq data at base-pair resolution performed by
+    derfinder
+License: Artistic-2.0
+LazyData: true
+URL: https://github.com/lcolladotor/derfinderReport
+biocViews: DifferentialExpression, HighThroughputSequencing, RNAseq, MultipleComparisons, Software
 Depends:
     R(>= 3.1.0),
     derfinder (>= 0.0.46)
@@ -19,8 +26,8 @@ Imports:
     ggbio,
     rCharts (>= 0.4.2),
     data.table,
-    knitr,
-    rmarkdown (>= 0.1.28),
+    knitr (>= 1.5.25),
+    rmarkdown (>= 0.1.62),
     knitrBootstrap (>= 1.0.0),
     knitcitations (>= 0.5.0),
     xtable,
@@ -30,11 +37,3 @@ Suggests:
     biovizBase,
     TxDb.Hsapiens.UCSC.hg19.knownGene,
     Cairo
-Description: Generate HTML reports for results from fast differential
-    expression analysis of RNA-seq data at base-pair resolution performed by
-    derfinder
-License: Artistic-2.0
-LazyData: true
-URL: https://github.com/lcolladotor/derfinderReport
-biocViews: DifferentialExpression, HighThroughputSequencing, RNAseq,
-    MultipleComparisons, Software

R/generateReport.R

@@ -91,11 +91,17 @@
 #' load(file.path("generateReport-example", "chr21", "optionsStats.Rdata"))
 #'
 #' ## Generate the HTML report
-#' generateReport(prefix="generateReport-example", browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, fullCov=list("21"=genomeDataRaw$coverage), optionsStats=optionsStats)
+#' report <- generateReport(prefix="generateReport-example", browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, fullCov=list("21"=genomeDataRaw$coverage), optionsStats=optionsStats)
 #'
-#' \dontrun{
+#'
+#' if(interactive()) {
 #' ## Browse the report
-#' browseURL(file.path("generateReport-example", "basicExploration", "basicExploration.html"))
+#' browseURL(report)
+#' }
+#'
+#' \dontrun{
+#' ## Note that you can run the example using:
+#' example("generateReport", "derfinderReport", ask=FALSE)
 #' }
 
 
@@ -237,12 +243,16 @@ generateReport <- function(prefix, outdir="basicExploration", output="basicExplo
 	cite_options(tooltip=TRUE)
 
 	## Fix citep
-	mycitep <- function(x) {
-		gsub("  </p>", "", citep(x))
+	mycitep <- function(x, short=NULL) {
+		res <- gsub("  </p>", "", citep(x))
+		if(!is.null(short)) {
+			res <- gsub("></a>", paste0(">", short, "</a>"), res)
+		}		
+		return(res)
 	}
 
 	## Write bibliography information
-	write.bibtex(c("knitcitations" = citation("knitcitations"), "derfinder" = citation("derfinder"), "derfinderReport" = citation("derfinderReport"), "knitrBootstrap" = citation("knitrBootstrap"), "ggbio" = citation("ggbio"), "ggplot2" = citation("ggplot2"), "rCharts" = citation("rCharts"), "knitr" = citation("knitr")[3]), file = file.path(prefix, outdir, "references.bib"))
+	write.bibtex(c("knitcitations" = citation("knitcitations"), "derfinder" = citation("derfinder"), "derfinderReport" = citation("derfinderReport"), "knitrBootstrap" = citation("knitrBootstrap"), "ggbio" = citation("ggbio"), "ggplot2" = citation("ggplot2"), "rCharts" = citation("rCharts"), "knitr" = citation("knitr")[3], "rmarkdown" = citation("rmarkdown")), file = file.path(prefix, outdir, "references.bib"))
 	bib <- read.bibtex(file.path(prefix, outdir, "references.bib"))
 
 	## Load files

README.md

@@ -15,10 +15,15 @@ Get R 3.1.0 or newer from [CRAN](http://cran.r-project.org/).
 ## If needed
 install.packages("devtools")
 
+## Note that knitr 1.5.25 is currently not available via CRAN
+## Following https://github.com/yihui/knitr
+install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),
+                 type = 'source')
+				 
 ## Pre-requisites from CRAN
-install.packages(c("knitr", "ggplot2", "gridExtra", "data.table", "knitr", "knitcitations",
-	"xtable", "RColorBrewer"))
-
+install.packages(c("xtable", "ggplot2", "gridExtra", "data.table", "knitcitations",
+	"RColorBrewer"))
+	
 ## You might need to install the Cairo package, but that will depend on the device you use
 ## for the plots
 install.packages("Cairo")
@@ -28,9 +33,9 @@ source("http://bioconductor.org/biocLite.R")
 biocLite(c("IRanges", "GenomicRanges", "biovizBase", "ggbio", "TxDb.Hsapiens.UCSC.hg19.knownGene"))
 
 ## GitHub dependencies
-library(devtools)
-install_github('rstudio/rmarkdown')
-install_github('jimhester/knitrBootstrap')
+library("devtools")
+install_github("rstudio/rmarkdown")
+install_github("jimhester/knitrBootstrap")
 install_github("rCharts", "ramnathv", ref="dev")
 install_github("derfinder", "lcolladotor")
 

inst/basicExploration/basicExploration.Rmd

@@ -307,7 +307,7 @@ t1$print("regions", cdn=TRUE)
 
 # Best region clusters
 
-The following plots were made using `ggbio` `r mycitep(bib[["ggbio"]])` which in turn uses `ggplot2` `r mycitep(bib[["ggplot2"]])`. For more details check `plotRegion` in `derfinder` `r mycitep(bib[["derfinder"]])`. 
+The following plots were made using `ggbio` `r mycitep(bib[["ggbio"]])` which in turn uses `ggplot2` `r mycitep(bib[["ggplot2"]])`. For more details check `plotCluster()` in `derfinder` `r mycitep(bib[["derfinder"]])`. 
 
 ## Plots
 
@@ -423,7 +423,7 @@ t2$print("permutation")
 
 # Bibliography
 
-This report is part of `derfinder` `r mycitep(bib[["derfinder"]])` and was generated using `knitr` `r mycitep(bib[["knitr"]])` and styled via `knitrBootstrap` `r mycitep(bib[["knitrBootstrap"]])`.
+This report is part of `derfinder` `r mycitep(bib[["derfinder"]])` and was generated using `knitrBootstrap` `r mycitep(bib[["knitrBootstrap"]])` with `knitr` `r mycitep(bib[["knitr"]])` and `rmarkdown` `r mycitep(bib[["rmarkdown"]], "JJ Allaire et al, 2014")` running behind the scenes.
 
 Citations made with `knitcitations` `r mycitep(bib[["knitcitations"]])`.
 

man/generateReport.Rd

@@ -151,11 +151,17 @@ mergeResults(chrnums="21", prefix="generateReport-example", genomicState=genomic
 load(file.path("generateReport-example", "chr21", "optionsStats.Rdata"))
 
 ## Generate the HTML report
-generateReport(prefix="generateReport-example", browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, fullCov=list("21"=genomeDataRaw$coverage), optionsStats=optionsStats)
+report <- generateReport(prefix="generateReport-example", browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, fullCov=list("21"=genomeDataRaw$coverage), optionsStats=optionsStats)
 
-\dontrun{
+
+if(interactive()) {
 ## Browse the report
-browseURL(file.path("generateReport-example", "basicExploration", "basicExploration.html"))
+browseURL(report)
+}
+
+\dontrun{
+## Note that you can run the example using:
+example("generateReport", "derfinderReport", ask=FALSE)
 }
 }
 \author{