Merge branch 'release/v0.0.8'

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: scone
-Version: 0.0.7
+Version: 0.0.8-9000
 Title: Single Cell Overview of Normalized Expression data
-Description: scone is a package to compare and rank the performance of different normalization schemes in real single-cell RNA-seq datasets.
+Description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.
 Authors@R: c(person("Michael", "Cole", email = "mbeloc@gmail.com",
 	          role = c("aut", "cre", "cph")),
 	     person("Davide", "Risso", email = "risso.davide@gmail.com",
 	          role = c("aut", "cph")))
 Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]
 Maintainer: Michael Cole <mbeloc@gmail.com>
-Date: 2016-07-22
+Date: 2016-09-26
 License: file LICENSE
 Depends:
   R (>= 3.3)
@@ -23,16 +23,24 @@ Imports:
   edgeR,
   fpc,
   gplots,
+  grDevices,
+  hexbin,
   limma,
   MASS,
   matrixStats,
   mixtools,
-  grDevices,
+  RColorBrewer,
   boot,
   shiny,
   miniUI,
   rhdf5,
-  RUVSeq
+  RUVSeq,
+  DT,
+  NMF,
+  ggplot2,
+  plotly,
+  reshape2,
+  visNetwork
 Suggests:
   knitr,
   rmarkdown,

NAMESPACE

@@ -21,12 +21,24 @@ export(lm_adjust)
 export(make_design)
 export(metric_sample_filter)
 export(scone)
+export(sconeReport)
+export(scone_easybake)
 export(score_matrix)
+export(simple_FNR_params)
 import(BiocParallel)
 import(gplots)
+import(plotly)
+import(visNetwork)
 importFrom(DESeq,estimateSizeFactorsForMatrix)
+importFrom(DT,dataTableOutput)
+importFrom(DT,dataTableProxy)
+importFrom(DT,formatSignif)
+importFrom(DT,renderDataTable)
+importFrom(DT,selectRows)
 importFrom(EDASeq,betweenLaneNormalization)
 importFrom(MASS,glm.nb)
+importFrom(NMF,aheatmap)
+importFrom(RColorBrewer,brewer.pal)
 importFrom(RUVSeq,RUVg)
 importFrom(aroma.light,normalizeQuantileRank.matrix)
 importFrom(boot,inv.logit)
@@ -36,14 +48,33 @@ importFrom(cluster,silhouette)
 importFrom(diptest,dip.test)
 importFrom(edgeR,calcNormFactors)
 importFrom(fpc,pamk)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_violin)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,guides)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,ylim)
 importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,pdf)
 importFrom(graphics,abline)
 importFrom(graphics,arrows)
 importFrom(graphics,barplot)
 importFrom(graphics,hist)
+importFrom(graphics,legend)
+importFrom(graphics,lines)
 importFrom(graphics,par)
 importFrom(graphics,plot)
+importFrom(graphics,points)
 importFrom(graphics,text)
+importFrom(hexbin,hexbin)
+importFrom(hexbin,plot)
 importFrom(limma,lmFit)
 importFrom(matrixStats,colIQRs)
 importFrom(matrixStats,colMedians)
@@ -52,18 +83,42 @@ importFrom(miniUI,gadgetTitleBar)
 importFrom(miniUI,miniContentPanel)
 importFrom(miniUI,miniPage)
 importFrom(mixtools,normalmixEM)
+importFrom(reshape2,melt)
 importFrom(rhdf5,h5createFile)
 importFrom(rhdf5,h5ls)
 importFrom(rhdf5,h5read)
 importFrom(rhdf5,h5write)
 importFrom(rhdf5,h5write.default)
+importFrom(shiny,br)
 importFrom(shiny,brushedPoints)
+importFrom(shiny,column)
+importFrom(shiny,downloadHandler)
+importFrom(shiny,downloadLink)
+importFrom(shiny,fluidPage)
+importFrom(shiny,fluidRow)
+importFrom(shiny,h5)
+importFrom(shiny,h6)
+importFrom(shiny,helpText)
+importFrom(shiny,mainPanel)
 importFrom(shiny,observeEvent)
+importFrom(shiny,p)
 importFrom(shiny,plotOutput)
+importFrom(shiny,reactive)
 importFrom(shiny,renderPlot)
+importFrom(shiny,renderTable)
 importFrom(shiny,renderText)
 importFrom(shiny,runGadget)
+importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
+importFrom(shiny,sidebarLayout)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,sliderInput)
 importFrom(shiny,stopApp)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tableOutput)
+importFrom(shiny,tabsetPanel)
+importFrom(shiny,titlePanel)
+importFrom(shiny,updateSelectInput)
 importFrom(shiny,verbatimTextOutput)
 importFrom(stats,approx)
 importFrom(stats,as.formula)
@@ -86,3 +141,6 @@ importFrom(stats,quantile)
 importFrom(stats,quasibinomial)
 importFrom(stats,sd)
 importFrom(utils,capture.output)
+importFrom(utils,head)
+importFrom(utils,sessionInfo)
+importFrom(utils,write.table)

R/data.R

@@ -1,4 +1,4 @@
-#' Positive and negative control genes
+#' Positive and Negative Control Genes
 #'
 #' Sets of positive and negative control genes, useful for input in
 #' \code{\link{scone}}.
@@ -7,21 +7,34 @@
 #' normalization or for evaluation and ranking of the normalization strategies.
 #'
 #' @details The datasets are in the form of \code{data.frame}, with at least one
-#'   column containing the gene symbols and optionally a second column
+#'   column containing the gene symbols and (optionally) a second column
 #'   containing additional information (such as cortical layer or cell cycle
 #'   phase).
 #'
 #' @details Note that the gene symbols follow the mouse conventions (i.e.,
 #'   capitalized) or the human conventions (i.e, all upper-case), based on the
-#'   original pubblication. One can use the \code{\link[base]{toupper}},
+#'   original publication. One can use the \code{\link[base]{toupper}},
 #'   \code{\link[base]{tolower}}, and \code{\link[tools]{toTitleCase}} functions
-#'   to convert the symbols.
-#'
-#' @details The genes in \code{cortical_markers} are from Figure 3 of Molyneaux
-#'   et al. (2007). The genes in \code{housekeeping} are from Eisenberg and
-#'   Levanon (2003) and in \code{housekeeping_revised} are from Eisenberg and
-#'   Levanon (2013). The genes in \code{cellcycle_genes} are adapted from
-#'   Kowalczyk et al. (2015).
+#'   to convert symbols.
+#'
+#' @details Mouse gene symbols in \code{cortical_markers} are transcribed from Figure 3 of Molyneaux
+#'   et al. (2007): "laminar-specific expression of 66 genes within the neocortex." 
+#' 
+#' @details Human gene symbols in \code{housekeeping} are derived from the list of "housekeeping" (HK) genes from 
+#'   the cDNA microarray analysis of Eisenberg and Levanon (2003): "[HK genes] belong to the class of
+#'   genes that are EXPRESSED in all tissues." "... from 47 different human tissues and cell lines."
+#'     
+#' @details Human gene symbols in \code{housekeeping_revised} are from Eisenberg and Levanon (2013): "This list 
+#'  provided ... is based on analysis of next-generation sequencing (RNA-seq) data. At least one variant of these 
+#'  genes is expressed in all tissues uniformly... The RefSeq transcript according to which we deemed the gene 
+#'  'housekeeping' is given." Housekeeping exons satisfy "(i) expression observed in all tissues; (ii) low 
+#'  variance over tissues: standard-deviation [log2(RPKM)]<1; and (iii) no exceptional expression in any single
+#'  tissue; that is, no log-expression value differed from the averaged log2(RPKM) by two (fourfold) or more." 
+#'  "We define a housekeeping gene as a gene for which at least one RefSeq transcript has more than half of 
+#'  its exons meeting the previous criteria (thus being housekeeping exons)."
+#'   
+#' @details Gene symbols in \code{cellcycle_genes} represent a set of genes marking G1/S and G2/M. No reference
+#'  provided.
 #'
 #' @references Molyneaux, B.J., Arlotta, P., Menezes, J.R. and Macklis, J.D..
 #'   Neuronal subtype specification in the cerebral cortex. Nature Reviews
@@ -30,10 +43,6 @@
 #'   Trends in Genetics, 2003, 19(7):362-5.
 #' @references Eisenberg E, Levanon EY. Human housekeeping genes, revisited.
 #'   Trends in Genetics, 2013, 29(10):569-74.
-#' @references Kowalczyk, M.S., Tirosh, I., Heckl, D., Rao, T.N., Dixit, A.,
-#'   Haas, B.J., Schneider, R.K., Wagers, A.J., Ebert, B.L. and Regev, A.
-#'   Single-cell RNA-seq reveals changes in cell cycle and differentiation
-#'   programs upon aging of hematopoietic stem cells. Genome research, 2015.
 #'
 #' @name control_genes
 #'

R/sample_filtering.R

@@ -18,6 +18,7 @@
 #'
 #' @importFrom boot logit
 #' @importFrom matrixStats rowMedians
+#' @export
 #'
 simple_FNR_params = function(expr, pos_controls, fn_tresh = 0.01){
 
@@ -121,6 +122,8 @@ simple_FNR_params = function(expr, pos_controls, fn_tresh = 0.01){
 #'  fnr auc threshold.
 #'@param plot logical. Should a plot be produced?
 #'@param hist_breaks hist() breaks argument. Ignored if `plot=FALSE`.
+#'@param ... Arguments to be passed to methods.
+#'
 #'
 #'@return A list with the following elements: \itemize{ \item{filtered_nreads}{
 #'  Logical. Sample has too few reads.} \item{filtered_ralign}{ Logical. Sample
@@ -140,7 +143,7 @@ metric_sample_filter = function(expr, nreads = colSums(expr), ralign = NULL,
                                 mixture = TRUE, dip_thresh = 0.05,
                                 hard_nreads = 25000, hard_ralign = 15, hard_breadth = 0.2, hard_auc = 10,
                                 suff_nreads = NULL, suff_ralign = NULL, suff_breadth = NULL, suff_auc = NULL,
-                                plot = FALSE, hist_breaks = 10){
+                                plot = FALSE, hist_breaks = 10, ...){
 
   criterion_count = 0