heatmap output as ggplot object

pcastellanoescuder · Nov 26, 2024 · 09bb015 · 09bb015
1 parent 21017ce
commit 09bb015
Show file tree

Hide file tree

Showing 8 changed files with 23 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis
-Version: 1.17.5
+Version: 1.17.6
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",
@@ -50,6 +50,7 @@ Imports:
     ggplot2,
     ggrepel,
     glmnet,
+    grid,
     impute,
     janitor,
     limma,

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.17.5
+# POMA 1.17.6
 
 * Allow grouping variable selection in `PomaImpute`
 * New documentation

diff --git a/R/PomaHeatmap.R b/R/PomaHeatmap.R
@@ -8,10 +8,10 @@
 #' @param sample_names Logical. Indicates if sample names should be displayed or not. Default is TRUE.
 #' @param feature_names Logical. Indicates if feature names should be displayed or not. Default is FALSE.
 #' @param show_legend Logical. Indicates if legend should be displayed or not. Default is TRUE.
-#'
+#' 
 #' @export
 #'
-#' @return A heatmap plot.
+#' @return A `ggplot` object.
 #' @author Pol Castellano-Escuder
 #' 
 #' @examples 
@@ -33,7 +33,7 @@ PomaHeatmap <- function(data,
                         covs = NULL,
                         sample_names = TRUE,
                         feature_names = FALSE,
-                        show_legend = TRUE){
+                        show_legend = TRUE) {
 
   if(!is(data, "SummarizedExperiment")){
     stop("data is not a SummarizedExperiment object. \nSee POMA::PomaCreateObject or SummarizedExperiment::SummarizedExperiment")
@@ -48,7 +48,7 @@ PomaHeatmap <- function(data,
 
     heatmap_annotations <- ComplexHeatmap::HeatmapAnnotation(df = metadata, show_legend = show_legend)
 
-    suppressMessages(
+    poma_heatmap <- suppressMessages(
       ComplexHeatmap::Heatmap(plot_data, 
                               name = "Value", 
                               top_annotation = heatmap_annotations,
@@ -57,13 +57,21 @@ PomaHeatmap <- function(data,
                               show_heatmap_legend = show_legend)
     )
   } else {
-    suppressMessages(
+    poma_heatmap <- suppressMessages(
       ComplexHeatmap::Heatmap(plot_data, 
                               name = "Value", 
                               show_row_names = feature_names, 
                               show_column_names = sample_names,
                               show_heatmap_legend = show_legend)
     )
   }
+
+  # Convert to ggplot
+  hm_grob <- grid::grid.grabExpr(ComplexHeatmap::draw(poma_heatmap))
+  poma_heatmap <- ggplot2::ggplot() +
+    ggplot2::annotation_custom(hm_grob, xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf) +
+    ggplot2::theme_void()
+
+  return(poma_heatmap)
 }
 
diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ output: github_document
 | _BioC_ branch 	| Status 	| Version 	| Rank 	|
 |-	|-	|-	|-	|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) 	| [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) 	| [![BioC released version](https://img.shields.io/badge/release%20version-1.16.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.17.5-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.17.6-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
 
   <!-- badges: end -->
 

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                            | Rank                                                                                                                         |
 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.16.0-blue.svg)](https://www.bioconductor.org/packages/POMA)             | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.17.5-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.17.6-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
 
 <!-- badges: end -->
 

diff --git a/man/PomaHeatmap.Rd b/man/PomaHeatmap.Rd
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
diff --git a/tests/testthat/test-PomaHeatmap.R b/tests/testthat/test-PomaHeatmap.R
@@ -2,7 +2,7 @@
 test_that("PomaHeatmap handles valid SummarizedExperiment objects", {
   data <- create_mock_summarized_experiment()
   heatmap_plot <- PomaHeatmap(data)
-  expect_is(heatmap_plot, "Heatmap")
+  expect_is(heatmap_plot, "ggplot")
 })
 
 test_that("PomaHeatmap stops with non-SummarizedExperiment objects", {
@@ -13,18 +13,18 @@ test_that("PomaHeatmap stops with non-SummarizedExperiment objects", {
 test_that("PomaHeatmap handles covariates correctly", {
   data <- create_mock_summarized_experiment()
   heatmap_plot_with_covs <- PomaHeatmap(data, covs = c("group"))
-  expect_is(heatmap_plot_with_covs, "Heatmap")
+  expect_is(heatmap_plot_with_covs, "ggplot")
 })
 
 test_that("PomaHeatmap handles sample_names and feature_names parameters correctly", {
   data <- create_mock_summarized_experiment()
   heatmap_plot_with_names <- PomaHeatmap(data, sample_names = FALSE, feature_names = TRUE)
-  expect_is(heatmap_plot_with_names, "Heatmap")
+  expect_is(heatmap_plot_with_names, "ggplot")
 })
 
 test_that("PomaHeatmap handles show_legend parameter correctly", {
   data <- create_mock_summarized_experiment()
   heatmap_plot_no_legend <- PomaHeatmap(data, show_legend = FALSE)
-  expect_is(heatmap_plot_no_legend, "Heatmap")
+  expect_is(heatmap_plot_no_legend, "ggplot")
 })