The tidyHeatmap package

Stefano Mangiola 2025-01-26

tidyHeatmap is a package that introduces tidy principles to the creation of information-rich heatmaps. This package uses ComplexHeatmap as graphical engine.

Citation

Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472

Please have a look also to

• tidygate for adding custom gate information to your tibble
• tidySingleCellExperiment for tidy manipulation of Seurat objects
• tidyseurat for tidy manipulation of Seurat objects
• tidybulk for tidy high-level data analysis and manipulation
• tidySummarizedExperiment for heatmaps produced with tidy principles

Full documentation here

# Create some more data points
pasilla_plus <- 
	tidyHeatmap::pasilla |>
	dplyr::mutate(activation_2 = activation, activation_3 = activation) |> 
	tidyr::nest(data = -sample) |>
	dplyr::mutate(size = rnorm(n(), 4,0.5)) |>
	dplyr::mutate(age = runif(n(), 50, 200)) |>
	tidyr::unnest(data) 

# Plot
pasilla_plus |>
	heatmap(
		.column = sample,
		.row = symbol,
		.value = `count normalised adjusted`,	
		scale = "row"
	) |>
	annotation_tile(condition) |>
	annotation_point(activation) |>
	annotation_numeric(activation_3) |>
	annotation_tile(activation_2) |>
	annotation_bar(size) |>
	annotation_line(age)

Advantages:

• Modular annotation with just specifying column names
• Custom grouping of rows is easy to specify providing a grouped tbl. For example df |> group_by(...)
• Labels size adjusted by row and column total number
• Default use of Brewer and Viridis palettes

Functions/utilities available

Function	Description
heatmap	Plots base heatmap
group_by	dplyr function - groups heatpmap rows/columns
annotation_tile	Adds tile annotation to the heatmap
annotation_point	Adds point annotation to the heatmap
annotation_bar	Adds bar annotation to the heatmap
annotation_numeric	Adds bar + number annotation to the heatmap
annotation_line	Adds line annotation to the heatmap
layer_text	Add layer of text on top of the heatmap
layer_point	Adds layer of symbols on top of the heatmap
layer_square	Adds layer of symbols on top of the heatmap
layer_diamond	Adds layer of symbols on top of the heatmap
layer_arrow_up	Adds layer of symbols on top of the heatmap
layer_arrow_down	Add layer of symbols on top of the heatmap
layer_star	Add layer of symbols on top of the heatmap
layer_asterisk	Add layer of symbols on top of the heatmap
split_rows	Splits the rows based on the dendogram
split_columns	Splits the columns based on the dendogram
save_pdf	Saves the PDF of the heatmap
+	Integrate heatmaps side-by-side
as_ComplexHeatmap	Convert the tidyHeatmap output to ComplexHeatmap for non-standard “drawing”
wrap_heatmap	Allows the integration with the patchwork package

Installation

To install the most up-to-date version

devtools::install_github("stemangiola/tidyHeatmap")

To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage)

install.packages("tidyHeatmap")

Contribution

If you want to contribute to the software, report issues or problems with the software or seek support please open an issue here