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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

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:

Modular annotation with just specifying column names
Custom grouping of rows/columns is easy to specify with annotation_group, e.g. heatmap(...) |> annotation_group(...)
Labels size adjusted by row and column total number
Default use of Brewer and Viridis palettes

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.