Merge pull request #500 from ropensci/fix/CRAN-release

Fix/cran release

Author: cpsievert

.Rbuildignore

@@ -4,3 +4,4 @@
 ^data-raw$
 CONDUCT.md
 CONTRIBUTING.md
+build_site.R

.gitignore

@@ -4,3 +4,6 @@ Rapp.history
 *.RData
 *.Rproj.user
 .Rproj.user
+build_site.R
+inst/examples/*/*.html
+inst/examples/*/rsconnect/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: plotly
-Title: Create Interactive Web Graphics via Plotly's JavaScript Graphing Library
-Version: 3.3.1
+Title: Create Interactive Web Graphics via 'plotly.js'
+Version: 3.3.2
 Authors@R: c(person("Carson", "Sievert", role = c("aut", "cre"),
     email = "cpsievert1@gmail.com"),
     person("Chris", "Parmer", role = c("aut", "cph"),
@@ -16,7 +16,7 @@ Authors@R: c(person("Carson", "Sievert", role = c("aut", "cre"),
     person("Pedro", "Despouy", role = "aut",
     email = "pedro@plot.ly"))
 License: MIT + file LICENSE
-Description: Easily translate ggplot2 graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.
+Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
 URL: https://plot.ly/r, https://github.com/ropensci/plotly
 BugReports: https://github.com/ropensci/plotly/issues
 Depends:
@@ -47,7 +47,8 @@ Suggests:
     RColorBrewer,
     Rserve,
     RSclient,
-    broom
+    broom,
+    hexbin
 LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 5.0.1

NAMESPACE

@@ -21,10 +21,12 @@ S3method(to_basic,GeomDensity)
 S3method(to_basic,GeomDensity2d)
 S3method(to_basic,GeomErrorbar)
 S3method(to_basic,GeomErrorbarh)
+S3method(to_basic,GeomHex)
 S3method(to_basic,GeomHline)
 S3method(to_basic,GeomJitter)
 S3method(to_basic,GeomLine)
 S3method(to_basic,GeomLinerange)
+S3method(to_basic,GeomMap)
 S3method(to_basic,GeomPointrange)
 S3method(to_basic,GeomRaster)
 S3method(to_basic,GeomRect)

NEWS

@@ -1,4 +1,18 @@
-3.3.1 -- 10 Mar 2015
+3.4.0 -- 12 Mar 2016
+
+NEW FEATURES:
+
+* geom_map() and geom_hex() are now supported.
+
+CHANGES:
+
+* The default value of the fileopt argument was changed from "new" to "overwrite".
+
+BUGFIX:
+
+* Made a number of bugfixes/improvements to hoverinfo & conversion of geom_tile()/geom_point().
+
+3.3.1 -- 10 Mar 2016
 
 CHANGES:
 
@@ -8,13 +22,13 @@ BUGFIX:
 
 * Redundant legend entries are no longer shown.
 
-3.2.1 -- 10 Mar 2015
+3.2.1 -- 10 Mar 2016
 
 BUGFIX:
 
 * Proper formatting for date tooltips.
 
-3.2.0 -- 10 Mar 2015
+3.2.0 -- 10 Mar 2016
 
 CHANGES:
 
@@ -27,14 +41,14 @@ NEW FEATURES:
 * geom_violin() is now supported.
 * ggplotly() gains a mapping argument to control the set of aesthetics to appears in the tooltip as well as their order.
 
-3.1.0 -- 8 Mar 2015
+3.1.0 -- 8 Mar 2016
 
 CHANGES:
 
 * The "hidden" sharing option in plotly_POST() was renamed to "secret".
 * The default value in the scale argument in plotly_IMAGE() is now 1.
 
-3.0.0 -- 8 Mar 2015
+3.0.0 -- 8 Mar 2016
 
 NEW FEATURES:
 
@@ -48,7 +62,7 @@ BUG FIXES:
 
 * ggplotly() now supports most of scale_*()/theme()/guides(). As a result, this fixes a lot of issues (#482, #481, #479, #476, #473, #460, #456, #454, #453, #447, #443, #434, #422, #421, #399, #379, #378, #357, #318, #316, #242, #232, #211, #203, #185, #184, #161). In order to support all of scale_x_*() an scale_y_*(), we always use linear axis types, and supply ticktext/tickvals to plotly.js. This has some unfortunate consequences on hoverformatting, which may be addressed in future releases of plotly.js -- https://github.com/plotly/plotly.js/issues/320
 
-2.5.0 -- 1 Mar 2015
+2.5.0 -- 1 Mar 2016
 
 NEW FEATURES
 
@@ -64,76 +78,76 @@ CHANGES
 The arguments filename, fileopt, world_readable in ggplotly() were removed as
 they should be provided to plotly_POST() instead. 
 
-2.4.4 -- 13 Feb 2015
+2.4.4 -- 13 Feb 2016
 
 as.widget() now returns htmlwidget objects untouched. See #449.
 
-2.4.3 -- 11 Feb 2015
+2.4.3 -- 11 Feb 2016
 
 Ensure that we always return HTTPS links. Fixes #455
 
-2.4.2 -- 9 Feb 2015
+2.4.2 -- 9 Feb 2016
 
 Fix for on-premise domain configuration. 
 
-2.4.1 -- 2 Feb 2015
+2.4.1 -- 2 Feb 2016
 
 Attach base_url in as.widget() so it works in multiple contexts
 
-2.4.0 -- 1 Feb 2015
+2.4.0 -- 1 Feb 2016
 
 * Pass plot configuration using ... to avoid conflicts in defaults/documentation
 * Upgrade to plotly.js 1.5.1
 
-2.3.4 -- 1 Feb 2015
+2.3.4 -- 1 Feb 2016
 
 Added a plotly_api_domain environment variable for configuring the API domain. Fixes #441
 
-2.3.3 -- 27 Jan 2015
+2.3.3 -- 27 Jan 2016
 
 Bump axis number for each trace matching a panel number. fixes #318
 
-2.3.2 -- 25 Jan 2015
+2.3.2 -- 25 Jan 2016
 
 More accurate list of data_array properties. Fixes #415
 
-2.3.1 -- 25 Jan 2015
+2.3.1 -- 25 Jan 2016
 
 More accurate conversion of path width. Fixes #373.
 
-2.3.0 -- 19 Jan 2015
+2.3.0 -- 19 Jan 2016
 
 Add sharing argument and deprecate world_readable. Fixes #332
 
-2.2.4 -- 18 Jan 2015
+2.2.4 -- 18 Jan 2016
 
 Fix for error in embed_notebook(). See #409.
 
-2.2.3 -- 18 Jan 2015
+2.2.3 -- 18 Jan 2016
 
 Fix for geom_vline(). See #402.
 
-2.2.2 -- 18 Jan 2015
+2.2.2 -- 18 Jan 2016
 
 Fix bar orientation when we detect geom_bar() + coord_flip() in ggplotly(). Fixes #390.
 
-2.2.1 -- 18 Jan 2015
+2.2.1 -- 18 Jan 2016
 
 Search for axis title in scene object. fixes #393.
 
-2.2.0 -- 13 Jan 2015
+2.2.0 -- 13 Jan 2016
 
 The default for layout.hovermode is now 'closest' for non-line scatter traces
 
-2.1.3 -- 12 Jan 2015
+2.1.3 -- 12 Jan 2016
 
 Fix size and alpha translation for geom_point. Fixes #386
 
-2.1.2 -- 11 Jan 2015
+2.1.2 -- 11 Jan 2016
 
 Upgraded to plotlyjs 1.4.1. For a list of changes, see https://github.com/plotly/plotly.js/releases/tag/v1.4.1
 
-2.1.1 -- 11 Jan 2015
+2.1.1 -- 11 Jan 2016
 
 Upgraded to plotlyjs 1.4. For a list of changes, see https://github.com/plotly/plotly.js/releases/tag/v1.4.0
 

R/ggplotly.R

@@ -189,9 +189,8 @@ gg2list <- function(p, width = NULL, height = NULL, tooltip = "all", source = "A
     )
     # remove leading/trailing dots in "hidden" stat aes
     map <- sub("^\\.\\.", "", sub("\\.\\.$", "", map))
-    # TODO: allow users to specify a _list_ of mappings?
     if (!identical(tooltip, "all")) {
-      map <- map[names(map) %in% tooltip]
+      map <- map[tooltip]
     }
     # tooltips for discrete positional scales are misleading
     if (scales$get_scales("x")$is_discrete()) {
@@ -217,15 +216,20 @@ gg2list <- function(p, width = NULL, height = NULL, tooltip = "all", source = "A
         scaleName <- scales$get_scales(aesName)$scale_name
         # convert "milliseconds from the UNIX epoch" to a date/datetime
         # http://stackoverflow.com/questions/13456241/convert-unix-epoch-to-date-object-in-r
-        if ("datetime" %in% scaleName) forMat <- function(x) as.POSIXct(x / 1000, origin = "1970-01-01")
+        if ("datetime" %in% scaleName) forMat <- function(x) as.POSIXct(x, origin = "1970-01-01")
         # convert "days from the UNIX epoch" to a date/datetime
         if ("date" %in% scaleName) forMat <- function(x) as.Date(as.POSIXct(x * 86400, origin = "1970-01-01"))
-      } else {
-        if (aesName != "text") aesName <- paste0(aesName, "_plotlyDomain")
       }
       # add a line break if hovertext already exists
       if ("hovertext" %in% names(x)) x$hovertext <- paste0(x$hovertext, "<br>")
-      x$hovertext <- paste0(x$hovertext, varName, ": ", forMat(x[[aesName]]))
+      # text aestheic should be taken verbatim (for custom tooltips)
+      prefix <- if (identical(aesName, "text")) "" else paste0(varName, ": ")
+      # look for the domain, if that's not found, provide the range (useful for identity scales)
+      suffix <- tryCatch(
+        forMat(x[[paste0(aesName, "_plotlyDomain")]] %||% x[[aesName]]),
+        error = function(e) ""
+      )
+      x$hovertext <- paste0(x$hovertext, prefix, suffix)
     }
     x
   }, data, aesMap)

R/layers2traces.R

@@ -49,6 +49,7 @@ layers2traces <- function(data, prestats_data, layers, layout, scales, labels) {
       apply(d[idx], 1, paste, collapse = "@%&"),
       levels = apply(lvls, 1, paste, collapse = "@%&")
     )
+    if (all(is.na(fac))) fac <- 1
     dl <- split(d, fac, drop = TRUE)
     # list of traces for this layer
     trs <- Map(geom2trace, dl, paramz[i])
@@ -200,6 +201,20 @@ to_basic.GeomRect <- function(data, prestats_data, layout, params, ...) {
   prefix_class(data, "GeomPolygon")
 }
 
+#' @export
+to_basic.GeomMap <- function(data, prestats_data, layout, params, ...) {
+  common <- intersect(data$map_id, params$map$id)
+  data <- data[data$map_id %in% common, , drop = FALSE]
+  map <- params$map[params$map$id %in% common, , drop = FALSE]
+  # TODO: do we need coord_munch() as in GeomMap$draw_panel()
+  data$id <- data$map_id
+  data$map_id <- NULL
+  data$group <- NULL
+  data <- merge(data, map, by = "id", sort = FALSE)
+  data$group <- interaction(data[names(data) %in% c("PANEL", "group", "id")])
+  prefix_class(data, c("GeomPolygon", "GeomMap"))
+}
+
 #' @export
 to_basic.GeomRaster <- function(data, prestats_data, layout, params, ...) {
   data <- prefix_class(data, "GeomTile")
@@ -219,6 +234,23 @@ to_basic.GeomTile <- function(data, prestats_data, layout, params, ...) {
   }
 }
 
+#' @export
+to_basic.GeomHex <- function(data, prestats_data, layout, params, ...) {
+  # see ggplot2:::hexGrob
+  dx <- resolution(data$x, FALSE)
+  dy <- resolution(data$y, FALSE)/sqrt(3)/2 * 1.15
+  hexC <- hexbin::hexcoords(dx, dy, n = 1)
+  n <- nrow(data)
+  data$size <- ifelse(data$size < 1, data$size ^ (1 / 6), data$size ^ 6)
+  x <- rep.int(hexC$x, n) * rep(data$size, each = 6) + rep(data$x, each = 6)
+  y <- rep.int(hexC$y, n) * rep(data$size, each = 6) + rep(data$y, each = 6)
+  data <- data[rep(seq_len(n), each = 6), ]
+  data$x <- x
+  data$y <- y
+  data$group <- rep(seq_len(n), each = 6)
+  prefix_class(data, c("GeomPolygon", "GeomHex"))
+}
+
 #' @export
 to_basic.GeomContour <- function(data, prestats_data, layout, params, ...) {
   if (!"fill" %in% names(data)) data$fill <- NA
@@ -227,6 +259,10 @@ to_basic.GeomContour <- function(data, prestats_data, layout, params, ...) {
 
 #' @export
 to_basic.GeomDensity2d <- function(data, prestats_data, layout, params, ...) {
+  if ("hovertext" %in% names(data)) {
+    data$hovertext <- paste0(data$hovertext, "<br>")
+  }
+  data$hovertext <- paste0(data$hovertext, "Level: ", data$level)
   if (!"fill" %in% names(data)) data$fill <- NA
   prefix_class(data, "GeomPath")
 }
@@ -272,6 +308,7 @@ to_basic.GeomJitter <- function(data, prestats_data, layout, params, ...) {
   prefix_class(data, "GeomPoint")
 }
 
+
 #' @export
 to_basic.GeomErrorbar <- function(data, prestats_data, layout, params, ...) {
   # width for ggplot2 means size of the entire bar, on the data scale 
@@ -338,7 +375,6 @@ geom2trace.GeomPath <- function(data, params) {
     x = data$x,
     y = data$y,
     text = data$hovertext,
-    hoverinfo = "text",
     type = "scatter",
     mode = "lines",
     name = if (inherits(data, "GeomSmooth")) "fitted values",
@@ -380,7 +416,8 @@ geom2trace.GeomPoint <- function(data, params) {
   )
   # fill is irrelevant for pch %in% c(1, 15:20)
   pch <- uniq(data$shape) %||% params$shape %||% GeomPoint$default_aes$shape
-  if (any(pch %in% c(1, 15:20))) {
+  if (any(pch %in% c(1, 15:20)) ||
+      all(grepl("open$", shape)) && all(L$marker$color %in% "transparent")) {
     L$marker$color <- L$marker$line$color
   }
   L
@@ -432,8 +469,7 @@ geom2trace.GeomPolygon <- function(data, params) {
     )
   )
   if (inherits(data, "GeomSmooth")) {
-    L$name <- "standard error"
-    L$showlegend <- FALSE
+    L$hoverinfo <- "x+y"
   }
   L
 
@@ -491,27 +527,23 @@ geom2trace.GeomText <- function(data, params) {
 #' @export
 geom2trace.GeomTile <- function(data, params) {
   # make sure order of value make sense before throwing z in matrix
-  data <- data[order(data$x, order(data$y, decreasing = T)), ]
+  data <- data[order(order(data$x), data$y), ]
   x <- sort(unique(data$x))
   y <- sort(unique(data$y))
-  fill <- data$fill_plotlyDomain
-  colorscale <- cbind(
-    c(0, 1),
-    data[c(which.min(fill), which.max(fill)), "fill"]
-  )
+  fill <- scales::rescale(data$fill_plotlyDomain)
+  txt <- data$hovertext
+  # create the colorscale, which should ignore NAs
+  data <- data[!is.na(fill), ]
+  o <- data[order(data$fill_plotlyDomain), "fill"]
+  n <- length(o)
+  qs <- seq(0, 1, length.out = min(n, 100))
+  idx <- o[pmax(1, round(n * qs))]
+  colorscale <- cbind(qs, idx)
   list(
     x = x,
     y = y,
-    z = matrix(
-      scales::rescale(fill), 
-      nrow = length(y), 
-      ncol = length(x)
-    ),
-    text = matrix(
-      data$hovertext, 
-      nrow = length(y), 
-      ncol = length(x)
-    ),
+    z = matrix(fill, nrow = length(y), ncol = length(x)),
+    text = matrix(txt, nrow = length(y), ncol = length(x)),
     colorscale = colorscale,
     type = "heatmap",
     showscale = FALSE,
@@ -619,10 +651,10 @@ make_error <- function(data, params, xy = "x") {
   e <- list(
     x = data$x,
     y = data$y,
+    text = data$hovertext,
     type = "scatter",
     mode = "lines",
     opacity = 0,
-    hoverinfo = "none",
     line = list(color = color)
   )
   e[[paste0("error_", xy)]] <- list(