fix r check issues

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iheatmapr
 Type: Package
 Title: Interactive, Complex Heatmaps
-Version: 1.0.0
+Version: 1.0.0.9999
 Authors@R: c(person("Alicia", "Schep",
                   email = "aschep@gmail.com",
                   role = c("aut", "cre"),
@@ -49,7 +49,6 @@ Depends:
     R (>= 3.2.0)
 Imports:
     methods,
-    plyr,
     utils,
     magrittr,
     stats,
@@ -71,7 +70,7 @@ Suggests:
     roxygen2,
     covr,
     webshot
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 URL: https://docs.ropensci.org/iheatmapr (website) https://github.com/ropensci/iheatmapr
 BugReports: https://github.com/ropensci/iheatmapr/issues

NAMESPACE

@@ -76,6 +76,6 @@ importFrom(htmlwidgets,sizingPolicy)
 importFrom(jsonlite,toJSON)
 importFrom(knitr,knit_print)
 importFrom(magrittr,"%>%")
-importFrom(plyr,round_any)
 importFrom(scales,zero_range)
+importFrom(stats,setNames)
 importFrom(utils,modifyList)

R/colorbars.R

@@ -79,7 +79,6 @@ setup_colorbar_grid <- function(nrows = 3,
 }
 
 #' @importFrom scales zero_range
-#' @importFrom plyr round_any
 tickvals_helper <- function(zmin, zmid, zmax) {
 
   rng <- c(zmin, zmax)
@@ -92,12 +91,12 @@ tickvals_helper <- function(zmin, zmid, zmax) {
   }
 
   if (zmid > zmin && zmid < zmax){
-    out <- c(round_any(zmin,precision,ceiling), 
-             round_any(zmid,precision), 
-             round_any(zmax,precision,floor))
+    out <- c(round_multiple(zmin,precision,ceiling), 
+             round_multiple(zmid,precision), 
+             round_multiple(zmax,precision,floor))
   } else{
-    out <- c(round_any(zmin,precision,ceiling), 
-             round_any(zmax,precision,floor))
+    out <- c(round_multiple(zmin,precision,ceiling), 
+             round_multiple(zmax,precision,floor))
   }
 
   out

R/list_utils.R

@@ -1,49 +1,80 @@
+#' S4 List Utils for Iheatmap classes
+#' 
+#' These are utility methods for list-like classes in the package.
+#' @name iheatmap_list_utils
+#' @rdname iheatmap_list_utils
+#' @param x input
+#' @docType methods
+#' @aliases length,IheatmapList-method
+#' as.list,IheatmapList-method
+#' names,IheatmapList-method
+#' `names<-`,IheatmapList-method
+#' `$`,IheatmapList-method
+#' `$<-`,IheatmapList-method
+#' `[`,IheatmapList-method
+#' `[<-`,IheatmapList-method
+#' `[[`,IheatmapList-method
+#' `[[<-`,IheatmapList-method
+#' lapply,IheatmapList-method
+#' vapply,IheatmapList-method
+#' @importFrom stats setNames
+#' @keywords internal
+
 setMethod("length", "IheatmapList", function(x) length(x@listData))
 
 setAs("IheatmapList", "list", function(from) as.list(from))
 
+#' @rdname iheatmap_list_utils
 setMethod("as.list", "IheatmapList", function(x) {
   x@listData
 })
 
+#' @rdname iheatmap_list_utils
 setMethod("[", "IheatmapList", function(x, i) {
   x_subset <- x
   x_subset@listData <- x_subset@listData[i]
   x_subset
 })
 
+#' @rdname iheatmap_list_utils
 setReplaceMethod("[", "IheatmapList", function(x, i, value) {
   x@listData[i] <- value
   x
 })
 
+#' @rdname iheatmap_list_utils
 setMethod("[[", "IheatmapList", function(x, i) {
   x@listData[[i]]
 })
 
+#' @rdname iheatmap_list_utils
 setReplaceMethod("[[", "IheatmapList", function(x, i, value) {
   x@listData[[i]] <- value
   x
 })
 
-
+#' @rdname iheatmap_list_utils
 setMethod("$", "IheatmapList", function(x, name) x[[name, exact=FALSE]])
 
+#' @rdname iheatmap_list_utils
 setReplaceMethod("$", "IheatmapList",
                  function(x, name, value) {
                    x[[name]] <- value
                    x
                  })
 
+#' @rdname iheatmap_list_utils
 setMethod("names", "IheatmapList", function(x) names(x@listData))
 
+#' @rdname iheatmap_list_utils
 setReplaceMethod("names", "IheatmapList",
                  function(x, value) {
                    names(x@listData) <- value
                    x
                  })
 
-
+#' @rdname iheatmap_list_utils
+#' @param FUN function to apply to each element of x
 setMethod("lapply", "IheatmapList",
           function(X, FUN, ...)
           {
@@ -53,11 +84,14 @@ setMethod("lapply", "IheatmapList",
           }
 )
 
+#' @rdname iheatmap_list_utils
+#' @param FUN.VALUE template for return value from FUN
+#' @param USE.NAMES logical, use names?
+#' @param ... additional arguments
 setMethod("vapply", "IheatmapList",
           function(X, FUN, FUN.VALUE, ..., USE.NAMES = TRUE)
           {
             FUN <- match.fun(FUN)
-            #browser()
             ii <- setNames(seq_along(X), names(X))
             vapply(ii, function(i) do.call(FUN, c(X[[i]], list(...))), FUN.VALUE, USE.NAMES = USE.NAMES)
           }

R/utils.R

@@ -2,6 +2,11 @@
 #' @export
 magrittr::`%>%`
 
+# Similar to round_any function in plyr
+round_multiple <- function(x, precision, fun = round) {
+  fun(x / precision) * precision
+}
+
 # makes x based on colnames of mat if available
 # if not available, just uses 1 to number of columns
 default_x <- function(mat){