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The tidyHeatmap package

Stefano Mangiola 2025-01-26

Lifecycle:maturing DOI

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

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_group(location) |>
    annotation_tile(condition, show_legend = FALSE) |>
    annotation_point(activation) |>
    annotation_numeric(activation_3) |>
    annotation_tile(activation_2) |>
    annotation_bar(size) |>
    annotation_line(age)

Advantages:

Retrieve heatmap data and dendrograms

After creating a heatmap, you can extract the matrix and dendrograms exactly as they appear in the plot:

# Create heatmap
hm <- tidyHeatmap::N52 |>
  tidyHeatmap::heatmap(
    .row = symbol_ct,
    .column = UBR,
    .value = `read count normalised log`
  )

# Extract heatmap data as plotted
result <- hm |> get_heatmap_data()
ordered_matrix <- result$matrix        # Matrix with rows/columns in heatmap order
row_dendrogram <- result$row_dend      # Row dendrogram object
column_dendrogram <- result$column_dend # Column dendrogram object

# All have consistent row and column names
print(rownames(ordered_matrix))
print(labels(row_dendrogram))

Functions/utilities available

Function Description
heatmap Plots base heatmap
annotation_group Adds group annotation strips and grouping to the heatmap
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
get_heatmap_data Retrieves matrix and dendrograms exactly as plotted
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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.