@@ -1,6 +1,6 @@

 Package: ReportingTools

 Title: Tools for making reports in various formats

-Version: 2.5.2

+Version: 2.5.3

 Author: Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina

         Chaivorapol, Gabriel Becker, and Josh Kaminker

 Maintainer: Jason A. Hackney <hackney.jason@gene.com>, Gabriel Becker

@@ -9,7 +9,7 @@ Depends: methods, knitr

 Imports: Biobase,hwriter,Category,GOstats,limma(>=

         3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db,

         GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils,

-         DESeq2(>= 1.3.41), S4Vectors, IRanges, ggplot2, ggbio

+         DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges

 Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla,

 Type: Package

 LazyLoad: yes

@@ -14,7 +14,6 @@ importFrom(edgeR, topTags, cpm)

 importFrom(GOstats, termGraphs, inducedTermGraph, plotGOTermGraph)

 importFrom(DESeq2, results, resultsNames)

 importFrom(ggplot2, ggplot) #we don't actually need this, we just need to be able to do setOldClass and have ggplot2 listed in imports

-importFrom(S4Vectors, normalizeSingleBracketSubscript)

 importMethodsFrom(AnnotationDbi, select, summary, mget)

 importMethodsFrom(Category, summary, geneIdsByCategory, geneIdUniverse)

@@ -26,8 +26,9 @@ setMethod("publish",

         if(ncol(object) == 0)

             stop("No columns available in data.")

-        filter.columns <-

-          normalizeSingleBracketSubscript(filter.columns, object)

+        # filter.columns <-

+        #   normalizeSingleBracketSubscript(filter.columns, object)

+        filter.columns <- .normalizeSubscript(filter.columns, object)

         sort.class.map <- c(

             "numeric"   = "sort-num-robust",

@@ -21,9 +21,11 @@ setMethod("getDefaultColumnClasses",

         filter.columns = sapply(object, is.numeric), ...)

     {

-        filter.columns <- 

-          normalizeSingleBracketSubscript(filter.columns,object)

-    

+        # filter.columns <- 

+        #   normalizeSingleBracketSubscript(filter.columns, object)

+        filter.columns <- .normalizeSubscript(filter.columns, object)

+        # filter.columns <- which(filter.columns)

+        

         ## For all columns, get the appropriate CSS class for sorting the

         ## data type

         sort.class.map <- c(

@@ -280,3 +282,19 @@ setMethod("getDefaultColumnClasses",

     }

 )

+.normalizeSubscript <- function(i, x)

+{

+    if( is.logical(i) )

+    {

+        

+        i <- rep(i, length.out = length(x))

+        i <- which(i)

+        

+    } else if( is.character(i) || is.factor(i) )

+    {

+        

+        i <- match(i, names(x))

+        

+    }

+    i

+}

\ No newline at end of file

@@ -82,7 +82,11 @@ setMethod("toReportDF",

         resTab <- as.data.frame(object[

             which(object$pad < pvalueCutoff & 

             abs(object$log2FoldChange) > abs(lfc)), ])

-            

+        

+        if(nrow(resTab) < 1){

+            stop("No features meet selection criteria.\nTry changing the log-fold change or p-value cutoff.")

+        }

+        

         if(!is.null(sort.by) & sort.by %in% colnames(resTab))

             resTab <- resTab[order(resTab[, sort.by]), ]

@@ -20,6 +20,13 @@ test_1dataframe <- function(){

         "3 columns are returned for the default data.frame")

 }

+test_1nogenes <- function(){

+    minp <- min(ddsRes$padj, na.rm=TRUE) / 2

+    df <- try(toReportDF(ddsRes, n = 100, pvalueCutoff = minp, 

+        make.plots = FALSE), silent=TRUE)

+    checkTrue(class(df) == "try-error")

+}

+

 test_2objectToHTML <- function(){

     rv <- objectToHTML(ddsRes, rep=NULL, factor = ddsRes$condition, 

         n = 100, make.plots=FALSE)