fix docs and plot palettes

DESCRIPTION

@@ -46,7 +46,7 @@ Suggests:
     rmarkdown,
     BiocStyle
 Remotes:
-    nhejazi/biotmleData,
+    nhejazi/biotmleData
 VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 biocViews:

NAMESPACE

@@ -1,14 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(plot,bioTMLE)
-export()
 export(.biotmle)
 export(biomarkertmle)
 export(heatmap_ic)
 export(modtest_ic)
 export(rnaseq_ic)
 export(volcano_ic)
 exportClasses(bioTMLE)
+exportClasses(data.frame_OR_EList)
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importClassesFrom(limma,EList)
 importFrom(SummarizedExperiment,SummarizedExperiment)

R/biotmle.R

@@ -1,6 +1,10 @@
 utils::globalVariables(c("new"))
 
-#' Constructor for class union data.frame_OR_EList
+#' @title S4 class union data.frame_OR_EList
+#'
+#' @description Class union contaning \code{data.frame} and \code{limma::Elist},
+#'              used internally to handle situations when a returned object has
+#'              a type that cannot be guessed from the function call.
 #'
 #' @return fusion of classes \code{data.frame} and \code{EList}, used within
 #'         \code{.biotmle} by class \code{bioTMLE} to handle uncertainty in the
@@ -11,7 +15,7 @@ utils::globalVariables(c("new"))
 #'
 #' @export
 #'
-methods::setClassUnion("data.frame_OR_EList", c("data.frame", "EList"))
+setClassUnion(name = "data.frame_OR_EList", members = c("data.frame", "EList"))
 
 ################################################################################
 

R/plots.R

@@ -31,8 +31,8 @@
 #'
 plot.bioTMLE <- function(x, ..., type = "pvals_adj") {
 
-  pal1 <- wesanderson::wes_palette("GrandBudapest", 100, type = "continuous")
-  pal2 <- wesanderson::wes_palette("Darjeeling", type = "continuous")
+  pal1 <- wesanderson::wes_palette("Royal2", 100, type = "continuous")
+  pal2 <- wesanderson::wes_palette("Darjeeling2", type = "continuous")
 
   if(type == "pvals_raw") {
     p <- ggplot2::ggplot(as.data.frame(x@topTable), ggplot2::aes(P.Value))
@@ -104,8 +104,8 @@ volcano_ic <- function(biotmle, fc_bound = 3.0, pval_bound = 0.2) {
 
   stopifnot(class(biotmle) == "bioTMLE")
 
-  pal1 <- wesanderson::wes_palette("GrandBudapest", 100, type = "continuous")
-  pal2 <- wesanderson::wes_palette("Darjeeling", type = "continuous")
+  pal1 <- wesanderson::wes_palette("Royal2", 100, type = "continuous")
+  pal2 <- wesanderson::wes_palette("Darjeeling2", type = "continuous")
 
   tt_volcano <- as.data.frame(biotmle@topTable) %>%
     dplyr::arrange(adj.P.Val) %>%
@@ -207,7 +207,7 @@ heatmap_ic <- function(x, ..., design, FDRcutoff = 0.05, top = 25) {
 
   annot <- ifelse(design == 0, "Control", "Treated")
 
-  pal <- wes_palette("Zissou", 100, type = "continuous")
+  pal <- wes_palette("Moonrise3", 100, type = "continuous")
 
   superheat::superheat(as.matrix(biomarkerTMLEout_top), row.dendrogram = TRUE,
                        grid.hline.col = "white", force.grid.hline = TRUE,