pull request for 0.4.1

.gitignore

@@ -21,6 +21,9 @@
 ehthumbs.db
 Thumbs.db
 
+# test files
+tests/**/*.pdf
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggstackplot
 Title: Create Overlapping Stacked Plots
-Version: 0.4
+Version: 0.4.1
 Authors@R: 
   c(person(
       given = "Sebastian", family = "Kopf", 
@@ -11,7 +11,7 @@ Authors@R:
       given = "Tristan", family = "Caro", 
       email = "tristan.caro@colorado.edu", 
       role = c("aut"), 
-      comment = c(ORCID = "")),
+      comment = c(ORCID = "0000-0001-6177-7444")),
   person(
       given = "Jamie", family = "McFarlin", 
       email = "jamie.mcfarlin@uwyo.edu", 
@@ -27,6 +27,9 @@ Description:
   Easily create overlapping grammar of graphics plots for scientific data visualization. 
   This style of plotting is particularly common in climatology and oceanography research communities.
 License: MIT + file LICENSE
+URL: https://ggstackplot.kopflab.org/,
+    https://github.com/kopflab/ggstackplot
+BugReports: https://github.com/kopflab/ggstackplot/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NEWS.md

@@ -1,3 +1,10 @@
+# ggstackplot 0.4.1
+
+* clarify the behaviour of the `switch_axes` parameter for horizontal stackplots
+* fix issue #30 to enable transformed shared axes
+* update the features vignette (now called explore) with new examples
+* include an example of a horizontal stackplot in the README
+
 # ggstackplot 0.4.0
 
 This is the first public release adding all core ggstackplot functionality.

R/ggstackplot.R

@@ -2,7 +2,7 @@
 
 #' Stack a ggplot
 #'
-#' Use `ggstackplot()` to generate a stackplot. If you need more fine control, use `prepare_stackplot()` and `assemble_stackplot()` individually.
+#' Use `ggstackplot()` to generate a stackplot. If you need more fine control, use `prepare_stackplot()` and `assemble_stackplot()` individually. To explore examples of all the different features, check out the `vignette("explore", "ggstackplot")` or the [online documentation](https://ggstackplot.kopflab.org/dev/articles/explore.html).
 #'
 #' @details
 #' `ggstackplot()` stacks a ggplot template with the provided data and parameters. It returns a plot object generated by [cowplot::plot_grid()]).
@@ -15,15 +15,14 @@
 #' @param palette which color to make the plots defined with an RColorBrewer palette ([RColorBrewer::display.brewer.all()]). You can only use `color` or `palette` parameter, not both.
 #' @param both_axes whether to have the stacked axes on both sides (overrides alternate_axes and switch_axes)
 #' @param alternate_axes whether to alternate the sides on which the stacked axes are plotted
-#' @param switch_axes whether to switch the stacked axes. Not switching means the first plot in the lower left corner is always arranged like a regular ggplot with the y axis on the left and the x axis on the bottom (even if `alternate_axes = TRUE`). Setting `switch_axes = TRUE`, leads to the opposite, i.e. first plot in the lower corner has the variable axis on the other side (secondary in ggplot terms).
+#' @param switch_axes whether to switch the stacked axes. Not switching means that for vertical stacks the plot at the bottom has the y-axis always on the left side; and for horizontal stacks that the plot on the left has the x-axis on top. Setting `switch_axes = TRUE`, leads to the opposite.
 #' @param overlap fractional overlap between adjacent plots. The max of 1 means plots are perfectly overlaid. The min of 0 means there is no overlap. If providing multiple values, must be 1 less than the number of stacked plots (since it's describing the overlap/gap between adjacent plots). By default there is no overlap between plots
 #' @param simplify_shared_axis whether to simplify the shared axis to only be on the last plot (+ first plot if a duplicate secondary axis is set)
 #' @param shared_axis_size if simplify_shared_axes is true, this determines the size of the shared axis relative to the size of a single plot
 #' @param template a template plot (ggplot object) to use for the stacked plots
 #' @param add a list of ggplot component calls to add to specific panel plots, either by panel variable name (named list) or index (unnamed list)
 #' @param debug `r lifecycle::badge("experimental")` debug flag to print the stackplot tibble and gtable intermediates
 #' @examples
-#'
 #' # 1 step stackplot (most common use)
 #' mtcars |>
 #'   ggstackplot(
@@ -42,6 +41,10 @@
 #'   ) |>
 #'   assemble_stackplot(overlap = c(1, 0, 0.3))
 #'
+#' @examplesIf interactive()
+#' # many more examples available in the vignette
+#' vignette("explore", "ggstackplot")
+#'
 #' @export
 #' @returns `ggstackplot()` returns a ggplot with overlayed plot layers
 ggstackplot <- function(
@@ -199,7 +202,7 @@ create_stackplot_tibble <- function(
     .xvar = factor_in_order(names(x)),
     .yvar = factor_in_order(names(y))
   ) |>
-    dplyr::arrange(dplyr::desc(.data$.xvar), .data$.yvar)
+    dplyr::arrange(.data$.xvar, .data$.yvar)
 
   # do we have a valid length for color or palette?
   stopifnot("can only set either `color` or `palette`, not both" = is.na(color) | is.na(palette))
@@ -223,9 +226,13 @@ create_stackplot_tibble <- function(
       .axis_switch =
         if (both_axes) NA else
           calculate_axis_switch(
+            # Note: the reverse_factor and reverse = TRUE for 'vertical'
+            # plot are both needed to properly invert the order AND keep
+            # the first plot in the lower left (unless switch = TRUE)
             var =
-              if (!!direction == "horizontal") .data$.xvar
-              else reverse_factor(.data$.yvar),
+              if (!!direction == "vertical")
+                reverse_factor(.data$.yvar)
+              else .data$.xvar,
             alternate = {{ alternate_axes }},
             switch = {{ switch_axes }},
             reverse = !!direction == "vertical"
@@ -313,11 +320,21 @@ create_stackplot_gtables <- function(prepared_stackplot, overlap, simplify_share
       call = call)
   }
 
-  # combine plots and themes and assembel the gtables
+  # combine plots and themes and assemble the gtables
   gtables <- prepared_stackplot |>
     combine_plot_theme_add(simplify_shared_axis = simplify_shared_axis, include_adds = TRUE) |>
     tidyr::unnest("config") |>
-    dplyr::select(".var", ".direction", "plot_w_theme") |>
+    dplyr::select(".var", ".direction", "plot_w_theme")
+
+  # make sure horizontal panels are in the correct order
+  # (reverse since horizontal positioning is inverted relative to vertical
+  # given the combined plot coordinate system starts in lower left corner)
+  if(gtables$.direction[1] == "horizontal") {
+    gtables <- gtables |> dplyr::arrange(dplyr::desc(dplyr::row_number()))
+    overlap <- rev(overlap)
+  }
+
+  gtables <- gtables |>
     # could think about relative sizing here with size_adjust but that doesn't seem like a feature we need
     dplyr::mutate(
       size = 1,

R/helpers.R

@@ -35,8 +35,12 @@ make_color_axis_theme <- function(config) {
   theme_modify_axes(
     axis = if (config$.direction == "horizontal") "x" else "y",
     change_color = if (!is.na(config$.color)) config$.color else NULL,
-    remove_primary = !is.na(config$.axis_switch) && config$.axis_switch,
-    remove_secondary = !is.na(config$.axis_switch) && !config$.axis_switch
+    remove_primary = !is.na(config$.axis_switch) &&
+      ((config$.direction == "horizontal" && !config$.axis_switch) ||
+      (config$.direction == "vertical" && config$.axis_switch)),
+    remove_secondary = !is.na(config$.axis_switch) &&
+      ((config$.direction == "horizontal" && config$.axis_switch) ||
+         (config$.direction == "vertical" && !config$.axis_switch))
   ) +
     # make the shared axis uniform
     theme_modify_axes(
@@ -139,7 +143,8 @@ make_plot <- function(config, data, template) {
     }
     if (config$.direction == "vertical" && is.null(plot$scales$scales[[x_scale_idx]]$limits)) {
       # add limits
-      plot$scales$scales[[x_scale_idx]]$limits <- limits
+      plot$scales$scales[[x_scale_idx]]$limits <-
+        sort(plot$scales$scales[[x_scale_idx]]$transform(limits))
     }
   }
 
@@ -171,7 +176,8 @@ make_plot <- function(config, data, template) {
     }
     if (config$.direction == "horizontal" && is.null(plot$scales$scales[[y_scale_idx]]$limits)) {
       # add limits
-      plot$scales$scales[[y_scale_idx]]$limits <- c(config$.shared_axis_min, config$.shared_axis_max)
+      plot$scales$scales[[y_scale_idx]]$limits <-
+        sort(plot$scales$scales[[y_scale_idx]]$transform(limits))
     }
   }
 
@@ -411,12 +417,12 @@ calculate_axis_switch <- function(var, alternate, switch, reverse) {
   if (!alternate) {
     # no alternating axis
     return(rep(switch, length(var)))
-  } else if (!switch) {
-    # alternating axis not switched
-    return(var %% 2L == 0L)
-  } else {
+  } else if (switch) {
     # switched alternating axis
     return(var %% 2L == 1L)
+  } else {
+    # alternating axis not switched
+    return(var %% 2L == 0L)
   }
 }
 

README.Rmd

@@ -100,14 +100,79 @@ dataset$data |>
   )
 ```
 
-## Show me more
+## What about horizontal stacks?
 
-```{r economics, fig.height=6, message = FALSE}
+```{r, message = FALSE}
+# download some more data from PANGAEA
+dataset2 <- pangaear::pg_data(doi = "10.1594/PANGAEA.933277")[[1]]
+
+# show what some of these data look like
+dataset2$data[
+  c("Depth sed [m]", "Comp", "δ13C [‰ PDB] (mean, vs. VPDB)")] |>
+  head() |> knitr::kable()
+```
+
+Full citation:
+
+> `r dataset2$citation`
+
+```{r "geodata-horizontal", message = FALSE}
+library(dplyr)
 library(ggplot2)
+# provide a different base plot with shared graphics elements among all plots
+my_template <-
+  # it's a ggplot
+  ggplot() +
+  # use a path plot for all (to connect the data points by depth!)
+  geom_point() + geom_path() +
+  # we still want the default stackplot theme
+  theme_stackplot() +
+  # depth is commonly plotted in reverse
+  scale_y_reverse()
+
+# now make the horizontal stack through depth for 2 of the variables
+dataset2$data |> 
+  filter(Comp == "C19") |>
+  arrange(`Depth sed [m]`) |>
+  ggstackplot(
+    x = c(
+      "δ13C carb [‰ PDB]",
+      "n-C19 δ13C_org [‰]" = "δ13C [‰ PDB] (mean, vs. VPDB)"
+    ),
+    y = "Depth sed [m]",
+    palette = "Dark2",
+    overlap = 1,
+    template = my_template
+  )
+```
+
+```{r "geodata-horizontal-2", message = FALSE}
+# or show them side by side (note that this could also be achieved with
+# ggplot facets except for the fine-control and coloring of the different x-axes)
+dataset2$data |> 
+  filter(Comp == "C19") |>
+  arrange(`Depth sed [m]`) |>
+  ggstackplot(
+    x = c(
+      "δ13C carb [‰ PDB]",
+      "n-C19 δ13C_org [‰]" = "δ13C [‰ PDB] (mean, vs. VPDB)"
+    ),
+    y = "Depth sed [m]",
+    palette = "Dark2",
+    # no more overlap
+    overlap = 0, 
+    # fine-tune the axes to be on top and bottom
+    both_axes = TRUE,
+    template = my_template
+  )
+```
 
-# using the built-in economics dataset in ggplot2 to create a horizontal stack
-# instead of vertical and using many of the customization features available
-# with ggstackplot and ggplot2
+## Show me more
+
+```{r economics, fig.height=6, message = FALSE}
+# using the built-in economics dataset in ggplot2 to create a vertical stacke of
+# double axis plots using many of the customization features available with 
+# ggstackplot and ggplot2
 ggplot2::economics |>
   ggstackplot(
     # define shared x axis
@@ -180,4 +245,4 @@ ggplot2::economics |>
 
 ## What else can I do with ggstackplot?
 
-- check out the **[Features](https://ggstackplot.kopflab.org/articles/features.html)** vignette for full details on all available functionality
+- check out our **[Vignette](https://ggstackplot.kopflab.org/articles/explore.html)** to explore the package further with detailed examples for all the different features