add more examples

R/anno-gg.R

@@ -2,8 +2,7 @@
 #' @inheritParams ggfit
 #' @inheritParams new_anno
 #' @inherit new_anno return
-#' @seealso
-#' - [ggfit]
+#' @seealso [ggfit]
 #' @examples
 #' g <- ggplot(mpg, aes(displ, hwy, colour = class)) +
 #'     geom_point()
@@ -73,8 +72,6 @@ anno_gg <- function(gg, align_with = "full", clip = NULL, gt = NULL,
     )
 }
 
-#' @seealso
-#' - [ggfit2]
 #' @examples
 #' # anno_gg2-panel: margins = NULL -------
 #' ggheat(m,

R/ggfit.R

@@ -6,7 +6,7 @@
 #' @param clip One of `"on"`, `"inherit"`, or `"off"`, indicating whether to
 #' clip to the extent out of the viewport, inherit the clipping region from
 #' `vp`, or turn clipping off altogether. A logical value of `TRUE` corresponds
-#' to `"on"` and `FALSE` corresponds to `"off"`. A `NULL` means `"inherit"`.
+#' to `"on"` and `FALSE` corresponds to `"off"`. Default: `"inherit"`.
 #' @param margins Which margin to draw besides the plot in the `vp` viewport.
 #' This allows for a more precise adjustment of the `clip` feature. Allowed
 #' values are `r rd_elements(MARGINS)`, When set to `NULL`, it means clip =
@@ -79,15 +79,13 @@ ggfit <- function(gg, align_with = "full", clip = NULL, vp = NULL, gt = NULL) {
     assert_clip(clip)
     assert_s3_class(vp, "viewport", null_ok = TRUE)
     # we need a valid viewport to decide the `clip` argument
-    vp <- vp %||% grid::viewport()
+    vp <- vp %||% grid::viewport(clip = grid::current.viewport()$clip)
     margins <- setup_margins(clip, vp)
     .ggfit(gt, align_with, margins, vp = vp)
 }
 
 setup_margins <- function(clip, vp) {
-    if (is.null(vp)) {
-        if (is.null(clip) || identical(clip, "inherit")) clip <- vp$clip
-    }
+    if (is.null(clip) || identical(clip, "inherit")) clip <- vp$clip
     if (isTRUE(clip) || identical(clip, "on")) {
         NULL
     } else {
@@ -163,7 +161,7 @@ ggfit2 <- function(gg, align_with = "full",
 
 .ggfit <- function(gt, align_with, margins = MARGINS,
                    elements = GG_ELEMENTS, vp = NULL) {
-    if (is.null(vp)) vp <- grid::viewport()
+    vp <- vp %||% grid::viewport(clip = grid::current.viewport()$clip)
     grid::pushViewport(vp)
     on.exit(grid::popViewport())
     if (align_with == "full") {

README.Rmd

@@ -1,5 +1,7 @@
 ---
-output: github_document
+output: 
+  github_document:
+    toc: true
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->

README.md

@@ -1,4 +1,10 @@
 
+- [eheat](#eheat)
+  - [Installation](#installation)
+  - [ggheat](#ggheat)
+  - [gganno](#gganno)
+  - [`anno_gg` and `anno_gg2`](#anno_gg-and-anno_gg2)
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # eheat
@@ -535,3 +541,148 @@ draw(Heatmap(small_mat,
 ```
 
 <img src="man/figures/README-Heatmap_gganno-1.png" width="100%" />
+
+## `anno_gg` and `anno_gg2`
+
+Both function acts similar with other annotation function in
+ComplexHeatmap. Both accept a ggplot object and fit it in the
+ComplexHeatmap annotation area.
+
+``` r
+g <- ggplot(mpg, aes(displ, hwy, colour = class)) +
+  geom_point()
+m <- matrix(rnorm(100), 10)
+
+# anno_gg-panel: clip = "off" -------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "panel",
+      clip = "off",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg-panel-1.png" width="100%" />
+
+``` r
+# anno_gg-panel: clip = "on" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "panel",
+      clip = "on",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg-panel-clip-1.png" width="100%" />
+
+``` r
+# anno_gg-plot --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "plot",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg-plot-1.png" width="100%" />
+
+``` r
+
+# anno_gg-full --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "full",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg-plot-2.png" width="100%" />
+
+`anno_gg2` is the same with `anno_gg`, it differs in terms of its
+arguments, and allow more precise adjustment of the clip feature.
+
+``` r
+# anno_gg2-panel: margins = NULL -------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = NULL,
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg2-panel1-1.png" width="100%" />
+
+``` r
+# anno_gg2-panel: margins = "l" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = "l",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg2-panel2-1.png" width="100%" />
+
+``` r
+# anno_gg2-panel: margins = "r" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = "r",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg2-panel3-1.png" width="100%" />
+
+``` r
+# anno_gg2-plot ---------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "plot",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg2-plot-1.png" width="100%" />
+
+``` r
+# anno_gg2-full --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "full",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+<img src="man/figures/README-anno_gg2-full-1.png" width="100%" />

vignettes/eheat.Rmd

@@ -1,6 +1,8 @@
 ---
 title: "eheat"
-output: rmarkdown::html_vignette
+output: 
+  rmarkdown::html_vignette:
+    toc: true
 vignette: >
   %\VignetteIndexEntry{eheat}
   %\VignetteEngine{knitr::rmarkdown}
@@ -431,3 +433,123 @@ draw(Heatmap(small_mat,
 ), merge_legends = TRUE)
 ```
 
+## `anno_gg` and `anno_gg2`
+Both function acts similar with other annotation function in ComplexHeatmap.
+Both accept a ggplot object and fit it in the ComplexHeatmap annotation area.
+
+```{r anno_gg-panel, fig.height=4, fig.width=5}
+g <- ggplot(mpg, aes(displ, hwy, colour = class)) +
+  geom_point()
+m <- matrix(rnorm(100), 10)
+
+# anno_gg-panel: clip = "off" -------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "panel",
+      clip = "off",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg-panel-clip, fig.height=4, fig.width=5}
+# anno_gg-panel: clip = "on" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "panel",
+      clip = "on",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg-plot, fig.height=4, fig.width=5}
+# anno_gg-plot --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "plot",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+
+# anno_gg-full --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg(g, "full",
+      height = unit(3, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+`anno_gg2` is the same with `anno_gg`, it differs in terms of its arguments, and
+allow more precise adjustment of the clip feature.
+```{r anno_gg2-panel1, fig.height=4, fig.width=5}
+# anno_gg2-panel: margins = NULL -------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = NULL,
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg2-panel2, fig.height=4, fig.width=5}
+# anno_gg2-panel: margins = "l" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = "l",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg2-panel3, fig.height=4, fig.width=5}
+# anno_gg2-panel: margins = "r" --------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "panel",
+      margins = "r",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg2-plot, fig.height=4, fig.width=5}
+# anno_gg2-plot ---------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "plot",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```
+
+```{r anno_gg2-full, fig.height=4, fig.width=5}
+# anno_gg2-full --------------------
+ggheat(m,
+  top_annotation = HeatmapAnnotation(
+    ggplot = anno_gg2(g, "full",
+      height = unit(6, "cm"),
+      show_name = FALSE
+    )
+  )
+)
+```