update Docs

R/geom-draw.R

@@ -56,6 +56,7 @@ geom_draw <- function(draw = grid::nullGrob(), ...,
 #' @usage NULL
 #' @aliases GeomDraw
 #' @export
+#' @keywords internal
 GeomDraw <- ggplot2::ggproto(
     "GeomDraw", ggplot2::Geom,
     ## No required_aes

R/layout-.R

@@ -18,6 +18,7 @@ is.layout <- function(x) methods::is(x, "Layout")
 #' @param object A [layout_heatmap()] or [layout_stack()] object.
 #' @importFrom methods show
 #' @export
+#' @keywords internal
 methods::setMethod("show", "Layout", function(object) {
     print(object)
 })

R/layout-heatmap-.R

@@ -1,4 +1,4 @@
-#' Heatmap layout
+#' Put plots around a Heatmap
 #'
 #' `ggheatmap` is an alias of `layout_heatmap`.
 #'

_pkgdown.yml

@@ -1,4 +1,57 @@
 url: https://yunuuuu.github.io/ggalign/
+
 template:
   bootstrap: 5
   light-switch: true
+
+reference:
+- title: Building plot
+- subtitle: Adding elemnt
+  desc: >
+    All plots begin with a call to `ggheatmap()` or `ggstack`, supplying default 
+    data and aesthetic mappings, specified by `aes()`. You then add reordering 
+    the layout, or group the layout into panels, and add plots, layers, scales,
+    coords with `+`. To save a plot to disk, use `ggsave()`.
+  contents:
+  - layout-add
+  - layout-and
+  - build_patchwork
+
+- subtitle: Active context
+  desc: >
+    A Layout object may have multiple plots, you can choose where to add ggplot2 
+    elements with following functions.
+  contents:
+  - hmanno
+  - active
+  - activate
+
+- title: Plot Layout
+  desc: A Layout object defines how to place the plots.
+  contents:
+  - layout_heatmap
+  - layout_stack
+
+- title: Plot basics
+  desc: Add plots to layout
+  contents:
+  - ggalign
+  - ggpanel
+
+- title: Setup Layout
+  desc: Reordering obervations or Group into panels
+  contents:
+  - starts_with("align")
+
+- title: Extending ggplot2
+  desc: New ggplot2 geoms, stats, scales, and facets
+  contents:
+  - geom_draw
+
+- title: helpers
+  desc: A handful of helpers
+  contents:
+  - hclust2
+  - dendrogram_data
+  - is.ggheatmap
+  - is.ggstack

vignettes/layout-heatmap.Rmd

@@ -85,6 +85,7 @@ default `mapping` and `data`. You can add `ggplot2` elements as usual.
 ggheatmap(small_mat) + geom_point() + scale_fill_viridis_c()
 ```
 
+### Position scales
 For position scales, `limits` cannot be setted, and the internal will always
 reset it as the default. This is required to align the heatmap and annotation.
 ```{r}
@@ -195,13 +196,14 @@ ggheatmap(small_mat) +
   align_reorder()
 ```
 
+### Facets and Panel titles
 When working with facets, manual configuration of panel using the `facet_*`
 function is not possible since the internal will use `facet_grid` to set the
 row/column groups controlled by heatmap annotation. However, you can provide
 `facet_grid` or `facet_null` (if no panel) to control the other arguments
 except `rows` and `cols`. A common usage case is to change the panel strip text.
 
-THe default theme in `ggalign` removed the panel strip text, you can override
+The default theme in `ggalign` removed the panel strip text, you can override
 the behaviour with `theme(strip.text = element_text())`. This allows us to add
 the panel title appropriately in heatmaps or any heatmap annotation with plot.
 ```{r}