biocheck fixes

DESCRIPTION

@@ -17,6 +17,7 @@ Imports:
     data.table,
     checkmate,
     MASS,
+    htmltools,
     limma,
     lme4,
     preprocessCore,
@@ -46,7 +47,7 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, Normalization
 LazyData: true
 URL: http://msstats.org
 BugReports: https://groups.google.com/forum/#!forum/msstats
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Encoding: UTF-8
 NeedsCompilation: no
 Packaged: 2017-10-20 02:13:12 UTC; meenachoi

NAMESPACE

@@ -73,6 +73,9 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,plot.new)
 importFrom(graphics,title)
+importFrom(htmltools,div)
+importFrom(htmltools,save_html)
+importFrom(htmltools,tagList)
 importFrom(limma,squeezeVar)
 importFrom(lme4,lmer)
 importFrom(marray,maPalette)

R/dataProcessPlots.R

@@ -87,7 +87,7 @@
 #' @importFrom graphics axis image legend mtext par plot.new title plot
 #' @importFrom grDevices dev.off hcl pdf
 #' @importFrom plotly ggplotly style add_trace plot_ly subplot
-#' 
+#' @importFrom htmltools tagList div save_html
 #' 
 #' @export
 #' 

R/utils_groupcomparison_plots.R

@@ -61,6 +61,8 @@ colMax <- function(data) sapply(data, max, na.rm = TRUE)
 colMin <- function(data) sapply(data, min, na.rm = TRUE)
 
 #' Create colorkey for ggplot2 heatmap
+#' @param my.colors blocks
+#' @keywords internal
 .getColorKeyGGPlot2 = function(my.colors, blocks) {
     x.at = seq(-0.05, 1.05, length.out = 14)
     par(mar = c(3, 3, 3, 3), mfrow = c(3, 1), oma = c(3, 0, 3, 0))
@@ -75,6 +77,8 @@ colMin <- function(data) sapply(data, min, na.rm = TRUE)
 }
 
 #' Create colorkey for plotly heatmap
+#' @param my.colors blocks
+#' @keywords internal
 .getColorKeyPlotly = function(my.colors, blocks) {
     color.key.plot <- plotly::layout(
         plot_ly(type = "image", z = list(my.colors)),