Merge branch 'release/v1.1.3'

Author: mbcole

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: scone
-Version: 1.1.2
+Version: 1.1.3
 Title: Single Cell Overview of Normalized Expression data
 Description: SCONE is an R package for comparing and ranking the performance of
 	different normalization schemes for single-cell RNA-seq and other 

NAMESPACE

@@ -60,6 +60,7 @@ importFrom(grDevices,pdf)
 importFrom(graphics,abline)
 importFrom(graphics,arrows)
 importFrom(graphics,barplot)
+importFrom(graphics,boxplot)
 importFrom(graphics,hist)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
@@ -91,6 +92,7 @@ importFrom(stats,dist)
 importFrom(stats,dnbinom)
 importFrom(stats,fitted.values)
 importFrom(stats,glm)
+importFrom(stats,lm)
 importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
@@ -101,7 +103,10 @@ importFrom(stats,prcomp)
 importFrom(stats,quantile)
 importFrom(stats,quasibinomial)
 importFrom(stats,sd)
+importFrom(stats,setNames)
+importFrom(stats,var)
 importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(utils,sessionInfo)
+importFrom(utils,write.csv)
 importFrom(utils,write.table)

R/SCONE_DEFAULTS.R

@@ -33,7 +33,8 @@ TMM_FN = function(ei) {
   return(eo)
 }
 
-#' Relative log-expression (RLE; DESeq) scaling normalization wrapper function
+#' Relative log-expression (RLE; DESeq) scaling normalization wrapper
+#' function
 #' @importFrom edgeR calcNormFactors
 #' @details SCONE scaling wrapper for \code{\link[edgeR]{calcNormFactors}}).
 #' @export

R/sconeReport.R

@@ -24,6 +24,9 @@
 #'
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom rARPACK svds
+#' @importFrom graphics boxplot
+#' @importFrom utils write.csv
+#' @importFrom stats setNames var
 #' @export
 #'
 #' @return An object that represents the SCONE report app.
@@ -66,15 +69,15 @@ sconeReport = function(x, methods,
     stop("reshape2 package needed for sconeReport()")
   }
 
-  if (!require("plotly", quietly = TRUE)) {
+  if (!requireNamespace("plotly", quietly = TRUE)) {
     stop("plotly package needed for sconeReport()")
   }
 
-  if (!require("visNetwork", quietly = TRUE)) {
+  if (!requireNamespace("visNetwork", quietly = TRUE)) {
     stop("visNetwork package needed for sconeReport()")
   }
 
-  if (!require("ggplot2", quietly = TRUE)) {
+  if (!requireNamespace("ggplot2", quietly = TRUE)) {
     stop("ggplot2 package needed for sconeReport()")
   }
 
@@ -223,18 +226,18 @@ sconeReport = function(x, methods,
                             ),
                             shiny::tabPanel("PCA",
                                      shiny::br(),
-                                     shiny::p(paste0("This panel shows principal ",
+                                shiny::p(paste0("This panel shows principal ",
                                               "component analysis ",
                                               "(PCA) results",
                                               " on different subsets ",
                                               "of genes.")),
                                      shiny::br(),
-                                     shiny::h6("Variance Explained (All Genes)"),
+                                  shiny::h6("Variance Explained (All Genes)"),
                                      shiny::p(paste0("Use this plot",
                                               " to decide on the ",
                                               "dimensionality of the reduced",
                                               " spaced used for evaluation.")),
-                                     shiny::plotOutput("plot_scree",width = "650px",
+                                shiny::plotOutput("plot_scree",width = "650px",
                                                 height = "400px"),
                                      shiny::br(),
                                      shiny::h6("2D (All Genes)"),
@@ -264,7 +267,7 @@ sconeReport = function(x, methods,
                             ),
                             shiny::tabPanel("QC",
                                      shiny::br(),
-                                     shiny::p(paste0("This panel shows the absolute",
+                              shiny::p(paste0("This panel shows the absolute",
                                               " correlations between",
                                               " Principal",
                                               " Components (PCs) of",
@@ -326,7 +329,7 @@ sconeReport = function(x, methods,
                             ),
                             shiny::tabPanel("Control Genes",
                                      shiny::br(),
-                                     shiny::p(paste0("Heatmap of control genes, ",
+                                  shiny::p(paste0("Heatmap of control genes, ",
                                               "colored by all",
                                               " three categories.")),
                                      shiny::br(),
@@ -625,7 +628,7 @@ sconeReport = function(x, methods,
              fill = cc[sort(unique(factor(strat_col())))])
     })
 
-    output$plot3d_base <- shiny::renderPlotly({
+    output$plot3d_base <- plotly::renderPlotly({
       PC1 <- PC2 <- PC3 <- NULL
       df <- setNames(data.frame(pc_obj_base()$x[,1:3]),
                      c("PC1", "PC2", "PC3"))
@@ -665,7 +668,7 @@ sconeReport = function(x, methods,
       abs(cor(qc,pc_obj_base()$x))
     })
 
-    output$qccorPlot <- shiny::renderPlotly({
+    output$qccorPlot <- plotly::renderPlotly({
       metric <- value <- PC <- NULL
 
       df = reshape2::melt(cor_qc()[,1:input$dim])
@@ -696,7 +699,7 @@ sconeReport = function(x, methods,
              fill = cc[sort(unique(factor(strat_col())))])
     })
 
-    output$plot3d_qc <- shiny::renderPlotly({
+    output$plot3d_qc <- plotly::renderPlotly({
       if(ncol(pc_obj_qc()$x) >= 3){
         PC1 <- PC2 <- PC3 <- NULL
         df <- setNames(data.frame(pc_obj_qc()$x[,1:3]),