README.md

In tidyHeatmap: A Tidy Implementation of Heatmap

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

tidyHeatmap documentation built on April 13, 2025, 9:09 a.m.