v1.5.6 -- switch to rmarkdown as the default, use DT package

With rmarkdown v0.9.5 released today and described at http://blog.rstudio.org/2016/03/21/rmarkdown-v0-9-5/ it doesn't look like knitrBootstrap adds much anymore as commented by Jim Hester himself at jimhester/knitrBootstrap#68 (comment) With this in mind, I'm switching the default to rmarkdown instead of using knitrBootstrap. Specially because the version of knitrBootstrap I like to use is only available via GitHub and will probably never make it to CRAN. It might even make sense to completely drop the knitrBootstrap dependency, although I'll leave it for now since there is no immediate need to drop it. I'm also testing using the DT package for the datatables features instead of the JS code that was included before. This might not work on this commit but I'll get it to work soon anyway.
leekgroup · Mar 21, 2016 · e9d8aeb · e9d8aeb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: regionReport
 Type: Package
 Title: Generate HTML reports for exploring a set of regions
-Version: 1.5.5
+Version: 1.5.6
 Date: 2016-03-21
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "lcollado@jhu.edu"), person(c("Andrew", "E."), "Jaffe", role = "aut",
@@ -24,6 +24,7 @@ Imports:
     derfinder (>= 1.1.0),
     derfinderPlot (>= 1.3.2),
     devtools (>= 1.6),
+    DT,
     GenomeInfoDb,
     GenomicRanges,
     ggbio (>= 1.13.13),
@@ -36,10 +37,11 @@ Imports:
     knitrBootstrap (>= 0.9.0),
     mgcv,
     RColorBrewer,
-    rmarkdown (>= 0.3.3),
+    rmarkdown (>= 0.9.5),
     whisker
 Suggests:
     BiocStyle,
     biovizBase,
     Cairo,
     TxDb.Hsapiens.UCSC.hg19.knownGene
+RoxygenNote: 5.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(derfinderReport)
 export(derfinder_report)
@@ -7,6 +7,7 @@ export(render_report)
 export(templateDensity)
 export(templateManhattan)
 export(templatePvalueDensity)
+import(DT)
 import(GenomeInfoDb)
 import(GenomicRanges)
 import(IRanges)

diff --git a/R/derfinderReport.R b/R/derfinderReport.R
@@ -3,8 +3,8 @@
 #' This function generates a HTML report exploring the basic results from 
 #' single base-level approach derfinder analysis results 
 #' (www.bioconductor.org/packages/derfinder). The HTML report itself 
-#' is generated using knitrBoostrap which uses knitr (http://yihui.name/knitr/) 
-#' behind the scenes. It works best after using \link[derfinder]{mergeResults}.
+#' is generated using rmarkdown (http://rmarkdown.rstudio.com/). It works best 
+#' after using \link[derfinder]{mergeResults}.
 #' 
 #' @param prefix The main data directory path where 
 #' \link[derfinder]{mergeResults} was run. It should be the same as 
@@ -68,6 +68,7 @@
 #' @import knitcitations
 #' @import RColorBrewer
 #' @import mgcv
+#' @import DT
 #' @import GenomeInfoDb
 #' @importFrom devtools session_info
 #'
@@ -153,48 +154,48 @@ derfinderReport <- function(prefix, outdir = 'basicExploration',
     startTime <- Sys.time()
 
     ## Advanced parameters
-#' @param chrsStyle The naming style of the chromosomes. By default, UCSC. See 
-#' \link[GenomeInfoDb]{seqlevelsStyle}.    
+# @param chrsStyle The naming style of the chromosomes. By default, UCSC. See 
+# \link[GenomeInfoDb]{seqlevelsStyle}.    
     chrsStyle <- .advanced_argument('chrsStyle', 'UCSC', ...)
 
-#' @param species Species name. See \link[derfinder]{extendedMapSeqlevels}  for 
-#' more information.
+# @param species Species name. See \link[derfinder]{extendedMapSeqlevels}  for 
+# more information.
     species <- .advanced_argument('species', getOption('species', 'homo_sapiens'), ...)
 
-#' @param currentStyle Current naming style used. See 
-#' \link[derfinder]{extendedMapSeqlevels} for more information.
+# @param currentStyle Current naming style used. See 
+# \link[derfinder]{extendedMapSeqlevels} for more information.
     currentStyle <- .advanced_argument('currentStyle', 'UCSC', ...)
 
 
-#' @param fullRegions Part of the output of \link[derfinder]{mergeResults}. 
-#' Specify it only if you have already loaded it in memory.
+# @param fullRegions Part of the output of \link[derfinder]{mergeResults}. 
+# Specify it only if you have already loaded it in memory.
     fullRegions <- .advanced_argument('fullRegions', NULL, ...)
 
 
-#' @param fullNullSummary Part of the output of \link[derfinder]{mergeResults}. 
-#' Specify it only if you have already loaded it in memory.
+# @param fullNullSummary Part of the output of \link[derfinder]{mergeResults}. 
+# Specify it only if you have already loaded it in memory.
     fullNullSummary <- .advanced_argument('fullNullSummary', NULL, ...)
 
 
-#' @param fullAnnotatedRegions Part of the output of 
-#' \link[derfinder]{mergeResults}. Specify it only if you have already loaded 
-#' it in memory.
+# @param fullAnnotatedRegions Part of the output of 
+# \link[derfinder]{mergeResults}. Specify it only if you have already loaded 
+# it in memory.
     fullAnnotatedRegions <- .advanced_argument('fullAnnotatedRegions', NULL,
         ...)
 
 
-#' @param optionsStats Part of the output of \link[derfinder]{analyzeChr}. 
-#' Specify it only if you have already loaded it in memory.
+# @param optionsStats Part of the output of \link[derfinder]{analyzeChr}. 
+# Specify it only if you have already loaded it in memory.
     optionsStats <- .advanced_argument('optionsStats', NULL, ...)
 
 
-#' @param optionsMerge Part of the output of \link[derfinder]{mergeResults}. 
-#' Specify it only if you have already loaded it in memory.
+# @param optionsMerge Part of the output of \link[derfinder]{mergeResults}. 
+# Specify it only if you have already loaded it in memory.
     optionsMerge <- .advanced_argument('optionsMerge', NULL, ...)
 
 
-#' @param overviewParams A two element list with \code{base_size} and 
-#' \code{areaRel} that control the text size for the genomic overview plots.
+# @param overviewParams A two element list with \code{base_size} and 
+# \code{areaRel} that control the text size for the genomic overview plots.
     overviewParams <- .advanced_argument('overviewParam', list(base_size = 10,
         areaRel = 5), ...)
 
@@ -233,7 +234,7 @@ derfinderReport <- function(prefix, outdir = 'basicExploration',
         derfinder = citation('derfinder')[1],
         derfinderPlot = citation('derfinderPlot')[1],
         regionReport = citation('regionReport')[1],
-        knitrBootstrap = citation('knitrBootstrap'), 
+        DT = citation('DT'), 
         ggbio = citation('ggbio'),
         ggplot2 = citation('ggplot2'),
         knitr = citation('knitr')[3],
@@ -244,7 +245,7 @@ derfinderReport <- function(prefix, outdir = 'basicExploration',
 
     ## Assign short names
     names(bib) <- c('knitcitations', 'derfinder', 'derfinderPlot', 
-        'regionReport', 'knitrBootstrap', 'ggbio', 'ggplot2', 'knitr',
+        'regionReport', 'DT', 'ggbio', 'ggplot2', 'knitr',
         'rmarkdown')
 
     ## Load files
@@ -282,7 +283,7 @@ derfinderReport <- function(prefix, outdir = 'basicExploration',
     ## Are there significant regions?
     sigVar <- switch(significantVar, pvalue = 'significant', qvalue = 'significantQval', fwer = 'significantFWER')
     if(significantVar == 'fwer' & !fwerExist) {
-        warning('There are no FWER adjusted P-values, will use FDR adjsuted p-values instead.')
+        warning('There are no FWER adjusted P-values, will use FDR adjusted p-values instead.')
         significantVar <- 'significantQval'
     }
     pvalText <- switch(sigVar, significant = 'P-value', significantQval = 'FDR adjusted P-value', significantFWER = 'FWER adjusted P-value')
@@ -308,7 +309,7 @@ derfinderReport <- function(prefix, outdir = 'basicExploration',
         file.copy(template, to = paste0(output, '.Rmd'))
 
         ## Output format
-        output_format <- .advanced_argument('output_format', 'knitrBootstrap::bootstrap_document', ...)
+        output_format <- .advanced_argument('output_format', 'html_document', ...)
         outputIsHTML <- output_format %in% c('knitrBootstrap::bootstrap_document', 'html_document')
 
         ## Check knitrBoostrap version

diff --git a/R/regionReport-package.R b/R/regionReport-package.R
@@ -3,8 +3,8 @@
 #' Generate an HTML reports to explore a set of regions such as the
 #' results from annotation-agnostic expression analysis of RNA-seq data at 
 #' base-pair resolution performed by derfinder.
-#' The HTML report itself is generated using knitrBootstrap 
-#' (https://github.com/jimhester/knitrBootstrap).
+#' The HTML report itself is generated using rmarkdown 
+#' (http://rmarkdown.rstudio.com/).
 #'
 #' @name regionReport-package
 #' @aliases regionReport-package

diff --git a/R/renderReport.R b/R/renderReport.R
@@ -74,6 +74,7 @@
 #' @import mgcv
 #' @import GenomeInfoDb
 #' @import whisker
+#' @import DT
 #' @importFrom devtools session_info
 #'
 #' @examples
@@ -139,8 +140,8 @@ renderReport <- function(regions, project, pvalueVars = c('P-values' = 'pval'),
     if(hasCustomCode) stopifnot(length(customCode) == 1)
     if(!is.null(annotation)) stopifnot(nrow(annotation) == length(regions))
 
-    #' @param overviewParams A two element list with \code{base_size} and 
-    #' \code{areaRel} that control the text size for the genomic overview plots.
+    # @param overviewParams A two element list with \code{base_size} and 
+    # \code{areaRel} that control the text size for the genomic overview plots.
     overviewParams <- .advanced_argument('overviewParam', list(base_size = 10,
             areaRel = 5), ...)
 
@@ -200,7 +201,7 @@ renderReport <- function(regions, project, pvalueVars = c('P-values' = 'pval'),
         knitcitations = citation('knitcitations'), 
         regionReport = citation('regionReport')[1],
         derfinderPlot = citation('derfinderPlot')[1],
-        knitrBootstrap = citation('knitrBootstrap'), 
+        DT = citation('DT'), 
         ggbio = citation('ggbio'),
         ggplot2 = citation('ggplot2'),
         knitr = citation('knitr')[3],
@@ -214,7 +215,7 @@ renderReport <- function(regions, project, pvalueVars = c('P-values' = 'pval'),
 
     ## Assign short names
     names(bib) <- c('knitcitations', 'regionReport', 'derfinderPlot', 
-        'knitrBootstrap', 'ggbio', 'ggplot2', 'knitr', 'rmarkdown', 'whisker',
+        'DT', 'ggbio', 'ggplot2', 'knitr', 'rmarkdown', 'whisker',
         'bumphunter', 'derfinder') 
 
     ## Save the call
@@ -230,7 +231,7 @@ renderReport <- function(regions, project, pvalueVars = c('P-values' = 'pval'),
         file.copy(template, to = paste0(output, '.Rmd'))
 
         ## Output format
-        output_format <- .advanced_argument('output_format', 'knitrBootstrap::bootstrap_document', ...)
+        output_format <- .advanced_argument('output_format', 'html_document', ...)
         outputIsHTML <- output_format %in% c('knitrBootstrap::bootstrap_document', 'html_document')
 
         ## Check knitrBoostrap version

diff --git a/inst/CITATION b/inst/CITATION
@@ -13,7 +13,7 @@ c(
         ),
         year = 2015,
         url = "http://www.bioconductor.org/packages/release/bioc/html/regionReport.html",
-        note = pkgVer('regionReport', '1.5.5')
+        note = pkgVer('regionReport', '1.5.6')
     ),
     bibentry(bibtype="article",
             title = "derfinder: Software for annotation-agnostic RNA-seq differential expression analysis",

diff --git a/inst/basicExploration/basicExploration.Rmd b/inst/basicExploration/basicExploration.Rmd
@@ -2,7 +2,9 @@
 output:
   html_document:
     toc: true
-    theme: united
+    toc_float: true
+    code_folding: hide
+    theme: spacelab
   pdf_document:
       toc: true
   knitrBootstrap::bootstrap_document:
@@ -46,10 +48,12 @@ library('gridExtra')
 library('knitr')
 library('RColorBrewer')
 library('mgcv')
+library('DT')
 
 ## Working behind the scenes
 # library('knitcitations')
 # library('rmarkdown')
+## Optionally
 # library('knitrBootstrap')
 
 #### Code setup
@@ -167,7 +171,7 @@ qtable <- lapply(c(1e-04, 0.001, 0.01, 0.025, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5,
 })
 qtable <- do.call(rbind, qtable)
 if(outputIsHTML) {
-    kable(qtable, format = 'html', align = c('c', 'c'))
+    kable(qtable, format = 'markdown', align = c('c', 'c'))
 } else {
     kable(qtable)
 }
@@ -190,7 +194,7 @@ fwertable <- lapply(c(1e-04, 0.001, 0.01, 0.025, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5,
 })
 fwertable <- do.call(rbind, fwertable)
 if(outputIsHTML) {
-    kable(fwertable, format = 'html', align = c('c', 'c'))
+    kable(fwertable, format = 'markdown', align = c('c', 'c'))
 } else {
     kable(fwertable)
 }
@@ -381,7 +385,7 @@ This genomic overview plot shows the annotation region type for the __candidate_
 annoReg <- table(fullRegions$region, useNA='always')
 annoReg.df <- data.frame(Region=names(annoReg), Count=as.vector(annoReg))
 if(outputIsHTML) {
-    kable(annoReg.df, format = 'html', align=rep('c', 3))
+    datatable(annoReg.df, format = 'markdown', align=rep('c', 3))
 } else {
     kable(annoReg.df)
 }
@@ -428,7 +432,7 @@ colnames(info) <- c('Number of Overlapping States', 'Frequency')
 info$State <- gsub('\\..*', '', rownames(info))
 rownames(info) <- NULL
 if(outputIsHTML) {
-    kable(info, format = 'html', align=rep('c', 4))
+    kable(info, format = 'markdown', align=rep('c', 4))
 } else {
     kable(info)
 }
@@ -459,10 +463,6 @@ vennSig <- vennRegions(fullAnnotatedRegions, counts.col = 'blue',
 
 Below is an interactive table with the top `r min(nrow(regions.df), nBestRegions * 5)` regions (out of `r nrow(regions.df)`) as ranked by area. Inf and -Inf are shown as 1e100 and -1e100 respectively.
 
-```{r jsInfo, results='asis', eval = outputIsHTML, echo = FALSE}
-cat("<link rel='stylesheet' href='http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/css/jquery.dataTables.css' />
-<script src='http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/jquery.dataTables.min.js'></script>")
-```
 
 ```{r bestAreaInfo, results='asis'}
 topArea <- head(regions.df, nBestRegions * 5)
@@ -484,28 +484,14 @@ topArea <- replaceInf(topArea, grep('log2FoldChange|value|area',
 
 ## Make the table
 if(outputIsHTML) {
-    kable(topArea, format = 'html', table.attr='id="regions_table"')
+    datatable(topArea, options = list(pagingType='full_numbers', pageLength=50, scrollX='100%'))
 } else {
     ## Only print the top part if your output is a PDF file
     kable(head(topArea, 20))
 }
 ```
 
-```{r jsTable, results='asis', eval = outputIsHTML, echo = FALSE}
-cat('<script type="text/javascript" charset="utf-8">
-$(document).ready(function() {
-    $("#regions_table").dataTable({
-        "sPaginationType": "full_numbers",
-        "sScrollX": "100%"
-    });
-});
-</script>
-')
-```
-
-
-
-
+
 # Best region clusters
 
 The following plots were made using `ggbio` `r citep(bib[['ggbio']])` which in turn uses `ggplot2` `r citep(bib[['ggplot2']])`. For more details check `plotCluster()` in `derfinder` `r citep(bib[['derfinder']])`. 
@@ -623,26 +609,14 @@ The following table shows how the group labels were permuted. `r ifelse(usedPerm
 
 ```{r permuteTable, results='asis', eval=usedPermutations, echo=usedPermutations}
 if(outputIsHTML) {
-    kable(permuteDetail, format = 'html', table.attr='id="permutation_table"')
+    datatable(permuteDetail, options = list(pagingType='full_numbers', pageLength=50, scrollX='100%'))
 } else {
     ## Only print the top part if your output is a PDF file
     kable(head(permuteDetail, 20))
 }
 
 ```
 
-```{r jsTablePermute, results='asis', eval = outputIsHTML, echo = FALSE}
-cat('<script type="text/javascript" charset="utf-8">
-$(document).ready(function() {
-    $("#permutation_table").dataTable({
-        "sPaginationType": "full_numbers",
-        "sScrollX": "100%"
-    });
-});
-</script>
-')
-```
-
 ```{r child = customCode, eval = hasCustomCode}
 ```
 
@@ -701,8 +675,7 @@ session_info()
 
 # Bibliography
 
-This report was created with `regionReport` `r citep(bib[['regionReport']])` using `knitrBootstrap` `r citep(bib[['knitrBootstrap']])`
-to format the html while `knitr` `r citep(bib[['knitr']])` and `rmarkdown` `r citep(bib[['rmarkdown']])` were running behind the scenes.
+This report was created with `regionReport` `r citep(bib[['regionReport']])` using `rmarkdown` `r citep(bib[['rmarkdown']])` while `knitr` `r citep(bib[['knitr']])` and  `DT` `r citep(bib[['DT']])` were running behind the scenes.
 
 Citations made with `knitcitations` `r citep(bib[['knitcitations']])`. The [BibTeX](http://www.bibtex.org/) file can be found [here](`r paste0(output, '.bib')`).