Merge pull request #91 from stemangiola/dev

Dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyHeatmap
 Title: A Tidy Implementation of Heatmap
-Version: 1.5.1
+Version: 1.6.0
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",
@@ -45,7 +45,8 @@ Imports:
     grid,
     grDevices,
     lifecycle (>= 0.2.0),
-    dendextend
+    dendextend,
+    patchwork
 Suggests:
     spelling,
     testthat,
@@ -56,7 +57,8 @@ Suggests:
     qpdf,
     covr,
     roxygen2,
-    forcats
+    forcats,
+    ggplot2
 VignetteBuilder: 
     knitr
 RdMacros: 

NAMESPACE

@@ -14,18 +14,21 @@ export(save_pdf)
 export(scale_robust)
 export(split_columns)
 export(split_rows)
+export(wrap_heatmap)
 import(ComplexHeatmap)
 import(dplyr)
 import(grDevices)
 import(tidyr)
 importFrom(ComplexHeatmap,anno_barplot)
 importFrom(ComplexHeatmap,anno_lines)
 importFrom(ComplexHeatmap,anno_points)
+importFrom(ComplexHeatmap,draw)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(circlize,colorRamp2)
 importFrom(dendextend,cutree)
 importFrom(grDevices,colorRampPalette)
 importFrom(grid,gpar)
+importFrom(grid,grid.grabExpr)
 importFrom(grid,grid.points)
 importFrom(grid,unit)
 importFrom(grid,unit.c)
@@ -37,6 +40,7 @@ importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(methods,new)
 importFrom(methods,show)
+importFrom(patchwork,wrap_elements)
 importFrom(purrr,as_mapper)
 importFrom(purrr,map)
 importFrom(purrr,map2)

R/patchwork.R

@@ -0,0 +1,56 @@
+#' Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch
+#'
+#' In order to add tidyHeatmap (ComplexHeatmap) element to a patchwork they can be
+#' converted to a compliant representation using the `wrap_heatmap()` function.
+#' This allows you to position either grobs, ggplot objects, patchwork
+#' objects, or even base graphics (if passed as a formula) in either the full
+#' area, the full plotting area (anything between and
+#' including the axis label), or the panel area (only the actual area where data
+#' is drawn). 
+#'
+#' @importFrom patchwork wrap_elements
+#' @importFrom grid grid.grabExpr
+#' @importFrom ComplexHeatmap draw
+#' @importFrom methods show
+#'
+#' @param panel,plot,full A grob, ggplot, patchwork, formula, raster, or
+#' nativeRaster object to add to the respective area.
+#'
+#' @param clip Should the grobs be clipped if expanding outside its area
+#'
+#' @param ignore_tag Should tags be ignored for this patch. This is relevant
+#' when using automatic tagging of plots and the content of the patch does not
+#' qualify for a tag.
+#'
+#' @docType methods
+#' @rdname wrap_heatmap-method
+#' 
+#' @return A wrapped_patch object
+#'
+#' @export
+#'
+#' @examples
+#' 
+#' 
+#' tidyHeatmap::N52 |>
+#' tidyHeatmap::heatmap(
+#'  .row = symbol_ct,
+#'  .column = UBR,
+#'  .value = `read count normalised log`,
+#' ) |> 
+#' wrap_heatmap()
+#' 
+setGeneric(
+	"wrap_heatmap", 
+	function(panel = NULL, plot = NULL, full = NULL, clip = TRUE, ignore_tag = FALSE) standardGeneric("wrap_heatmap")
+)
+
+#' Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch
+#' 
+#' @docType methods
+#' @rdname wrap_heatmap-method
+#' 
+#' @return A wrapped_patch object
+setMethod("wrap_heatmap", "InputHeatmap", function(panel = NULL, plot = NULL, full = NULL, clip = TRUE, ignore_tag = FALSE){
+	patchwork::wrap_elements(grid::grid.grabExpr(ComplexHeatmap::draw(ComplexHeatmap::draw(methods::show(panel)))))
+})

R/utilities.R

@@ -1137,6 +1137,9 @@ combine_elements_with_the_same_name = function(x){
 
 	# Fix CRAN notes
 	my_class  = NULL
+	value = NULL
+	name = NULL
+	data = NULL
 
 	if(length(unlist(x))==0) return(unlist(x))
 	else {

README.md

@@ -109,7 +109,7 @@ mtcars_tidy <-
 mtcars_tidy
 ```
 
-    ## # A tibble: 288 x 5
+    ## # A tibble: 288 × 5
     ##    `Car name`       hp    vs Property Value[,1]
     ##    <chr>         <dbl> <dbl> <chr>        <dbl>
     ##  1 Mazda RX4       110     0 mpg          0.151
@@ -407,6 +407,11 @@ mtcars_tidy |>
 
 ``` r
 library(forcats)
+```
+
+    ## Warning: package 'forcats' was built under R version 4.1.2
+
+``` r
 mtcars_tidy |> 
     mutate(`Car name` = fct_reorder(`Car name`, `Car name`, .desc = TRUE)) %>% 
     heatmap(
@@ -446,3 +451,27 @@ mtcars_tidy |>
 ```
 
 ![](man/fragments/figures/unnamed-chunk-25-1.png)<!-- -->
+
+## Using patchwork to integrate heatmaps
+
+``` r
+library(ggplot2)
+library(patchwork)
+
+p_heatmap =
+    mtcars_tidy |> 
+    heatmap(
+        `Car name`, Property, Value, 
+            show_heatmap_legend = FALSE,
+        row_names_gp = gpar(fontsize = 7)
+    ) 
+
+p_ggplot = tibble(value = 1:10) %>% ggplot(aes(value)) + geom_density()
+
+wrap_heatmap(p_heatmap) + 
+    p_ggplot +
+    wrap_heatmap(p_heatmap) + 
+    plot_layout(width = c(1, 0.3, 1))
+```
+
+![](man/fragments/figures/unnamed-chunk-26-1.png)<!-- -->

man/fragments/intro.Rmd

@@ -376,3 +376,25 @@ mtcars_tidy |>
 	) 
 ```
 
+## Using patchwork to integrate heatmaps
+
+```{r}
+library(ggplot2)
+library(patchwork)
+
+p_heatmap =
+	mtcars_tidy |> 
+	heatmap(
+		`Car name`, Property, Value, 
+			show_heatmap_legend = FALSE,
+		row_names_gp = gpar(fontsize = 7)
+	) 
+
+p_ggplot = tibble(value = 1:10) %>% ggplot(aes(value)) + geom_density()
+
+wrap_heatmap(p_heatmap) + 
+	p_ggplot +
+	wrap_heatmap(p_heatmap) + 
+	plot_layout(width = c(1, 0.3, 1))
+
+```