Improve plot_ly

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.11.7
+Version: 1.11.8
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="[email protected]",
@@ -26,7 +26,6 @@ Imports:
     SummarizedExperiment,
     tibble,
     ggplot2,
-    plotly,
     magrittr,
     rlang,
     purrr,
@@ -58,7 +57,8 @@ Suggests:
     GGally,
     uwot,
     celldex,
-    dittoSeq
+    dittoSeq,
+    plotly
 VignetteBuilder: 
     knitr
 RdMacros:

NAMESPACE

@@ -21,7 +21,6 @@ S3method(mutate,SingleCellExperiment)
 S3method(nest,SingleCellExperiment)
 S3method(pivot_longer,SingleCellExperiment)
 S3method(plot_ly,SingleCellExperiment)
-S3method(plot_ly,default)
 S3method(print,SingleCellExperiment)
 S3method(pull,SingleCellExperiment)
 S3method(rename,SingleCellExperiment)
@@ -45,7 +44,6 @@ S3method(unite,SingleCellExperiment)
 S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(join_transcripts)
-export(plot_ly)
 export(tidy)
 export(unnest_single_cell_experiment)
 exportMethods(aggregate_cells)
@@ -111,7 +109,6 @@ importFrom(pillar,get_extent)
 importFrom(pillar,style_subtle)
 importFrom(pillar,tbl_format_header)
 importFrom(pkgconfig,get_config)
-importFrom(plotly,plot_ly)
 importFrom(purrr,as_mapper)
 importFrom(purrr,imap)
 importFrom(purrr,map)
@@ -156,6 +153,7 @@ importFrom(ttservice,aggregate_cells)
 importFrom(ttservice,bind_cols)
 importFrom(ttservice,bind_rows)
 importFrom(ttservice,join_features)
+importFrom(ttservice,plot_ly)
 importFrom(utils,data)
 importFrom(utils,packageDescription)
 importFrom(utils,tail)

R/plotly_methods.R

@@ -1,54 +1,14 @@
-#' @name plotly
-#' @rdname plotly
-#' @inherit plotly::plot_ly
+#' @name plot_ly
+#' @rdname plot_ly
+#' @inherit ttservice::plot_ly
 #' @return `plotly`
 #' 
-#' @examples
-#' # TODO
+#' @examples 
+#' data(pbmc_small)
+#' pbmc_small |> 
+#'     plot_ly(x = ~ nCount_RNA, y = ~ nFeature_RNA)
 #' 
-#' @importFrom plotly plot_ly
-#' @export
-plot_ly <- function(data=data.frame(), 
-    ..., type=NULL, name=NULL,
-    color=NULL, colors=NULL, alpha=NULL,
-    stroke=NULL, strokes=NULL, alpha_stroke=1,
-    size=NULL, sizes=c(10, 100),
-    span=NULL, spans=c(1, 20),
-    symbol=NULL, symbols=NULL,
-    linetype=NULL, linetypes=NULL,
-    split=NULL, frame=NULL,
-    width=NULL, height=NULL, source="A") {
-    UseMethod("plot_ly")
-}
-
-#' @rdname plotly
-#' @export
-plot_ly.default <- function(data=data.frame(), 
-    ..., type=NULL, name=NULL,
-    color=NULL, colors=NULL, alpha=NULL,
-    stroke=NULL, strokes=NULL, alpha_stroke=1,
-    size=NULL, sizes=c(10, 100),
-    span=NULL, spans=c(1, 20),
-    symbol=NULL, symbols=NULL,
-    linetype=NULL, linetypes=NULL,
-    split=NULL, frame=NULL,
-    width=NULL, height=NULL, source="A") {
-    data %>%
-        # This is a trick to not loop the call
-        drop_class("tbl_df") %>%
-        plotly::plot_ly(...,
-            type=type, name=name,
-            color=color, colors=colors, alpha=alpha,
-            stroke=stroke, strokes=strokes, alpha_stroke=alpha_stroke,
-            size=size, sizes=sizes,
-            span=span, spans=spans,
-            symbol=symbol, symbols=symbols,
-            linetype=linetype, linetypes=linetypes,
-            split=split, frame=frame,
-            width=width, height=height, source=source)
-}
-
-#' @rdname plotly
+#' @importFrom ttservice plot_ly
 #' @export
 plot_ly.SingleCellExperiment <- function(data=data.frame(), 
     ..., type=NULL, name=NULL, 
@@ -63,7 +23,7 @@ plot_ly.SingleCellExperiment <- function(data=data.frame(),
     data %>%
         # This is a trick to not loop the call
         as_tibble() %>%
-        plot_ly(...,
+        ttservice::plot_ly(...,
             type=type, name=name,
             color=color, colors=colors, alpha=alpha,
             stroke=stroke, strokes=strokes, alpha_stroke=alpha_stroke,