funkyheatmap: Visualising data frames with mixed data types


Robrecht Cannoodt*

Data Intuitive

VIB Center for Inflammation Research

Ghent University

Louise Deconinck*

VIB Center for Inflammation Research

Ghent University

Artuur Couckuyt*

VIB Center for Inflammation Research

Ghent University

Nikolay S. Markov*

Northwestern University

Luke Zappia

Helmholtz Munich

Technical University of Munich

Malte D. Luecken

Helmholtz Munich

Marta Interlandi

University of Muenster

Wouter Saelens†

École Polytechnique Fédérale de Lausanne (EPFL)

VIB Center for Inflammation Research

Ghent University

Yvan Saeys†

VIB Center for Inflammation Research

Ghent University

*: Shared first authors, †: shared last authors.


{funkyheatmap} is an innovative package designed to create publication-ready visualisations of data frames containing a mix of numerical and non-numerical data. Its user-friendly interface makes it easy to generate a visualisation simply by providing the data frame. At the same time, {funkyheatmap} also offers flexibility for advanced users to refine their visualisations through row- and column-specific parameters.

The package’s simplicity and customizability make it an ideal tool for exploring summarised results in a research setting. While it has been used extensively to visualise benchmarking results in single-cell omics (Saelens et al. 2019; Luecken et al. 2021, 2023; Yan and Sun 2022; Sang-aram et al. 2023), it’s designed to be versatile and applicable to a wide range of other domains.

{funkyheatmap} has been released on CRAN and PyPi, and is in the process of being ported to JavaScript (Preview available on npm).

Statement of need

Data visualisation is an essential part of data analysis by revealing patterns, trends, and relationships between variables. Packages like ggplot2 (Wickham 2009), Matplotlib (Hunter 2007) and D3.js (Bostock, Ogievetsky, and Heer 2011) offer an intuitive and flexible interface to generate tailor-made visualisations for many types of use cases, such as dot plots, bar charts, and heatmaps.

However, these visualisation tools require intricate scripts when visualising data frames with semantically mixed data types, such as textual, categorical, numerical and ratio data. Such data frames, as typically produced by benchmarking studies, require a combination of these heatmaps, dot plots, bar charts, pie charts and images to visualise results comprehensively and correctly. {funkyheatmap} addresses this limitation by offering a comprehensive and user-friendly solution for visualising mixed data types in data frames.

The utility of {funkyheatmap} was first demonstrated in Saelens et al. (2019) and Luecken et al. (2021), where the unique design concept of funky heatmaps was employed. Since the source code was not available as a standalone R package at that time, several publications adapted the {funkyheatmap} design concepts for their visualisations (Mereu et al. 2020; Pratapa et al. 2019), thus underlining the need for a reusable package for generating funky heatmaps. Since publishing {funkyheatmap} on CRAN, {funkyheatmap} has been used in several other benchmarking studies to visualise the end-results (Yan and Sun 2022; Sang-aram et al. 2023; Luecken et al. 2023), demonstrating its effectiveness and utility in the research community.


The {funkyheatmap} package offers many features designed to customise and enhance the data visualisation process at multiple levels.

The package supports various geometries (geom) to represent different data types per column (Table 1). For instance, numerical data can be represented effectively using a funkyrect (a rounded rectangle where both size and roundness are scaled based on the data) or bar geom, while measurement data can be displayed using a labelled rectangle geom. Categorical data can be visualised using a text or image geom, and proportional data can be represented using a pie-chart geom.

Categorical grouping of rows and columns is supported to separate semantically related rows (e.g. methods) and columns (e.g. metrics and features). It is possible to assign a hierarchical index and different colour palettes to the columns, making these semantic groups more explicit.

Table 1: Recommended geometries in {funkyheatmap} for different data types. The table presents the suggested visualisation methods (geoms) based on the data type of the columns. These recommendations provide a starting point for users to select the most appropriate visual representation for their specific data.
Data type Example Recommended geom
Numerical data Scores from 0 to 1 funkyrect
Aggregated data The mean of scores bar
Measurement data 3MB or 4h rect + text overlay
Categorical data R or Python text or image
Proportional data 80% success, 10% OOM, 10% failed pie


The following figure (Figure 1) illustrates the rich and comprehensive visualisations possible with {funkyheatmap}, showcasing its capacity to intuitively represent mixed data types in a single heatmap. The heatmap incorporates different geometries, categorical groupings, and colour palettes, providing a clear, informative, and aesthetically pleasing representation of the data.


  data = dynbenchmark_data$data,
  column_info = dynbenchmark_data$column_info,
  column_groups = dynbenchmark_data$column_groups,
  row_info = dynbenchmark_data$row_info,
  row_groups = dynbenchmark_data$row_groups,
  palettes = dynbenchmark_data$palettes,
  col_annot_offset = 3.2

Figure 1: An example of a {funkyheatmap} visualisation using data from a benchmarking study of trajectory inference methods (Saelens et al. 2019).


The {funkyheatmap} visualisation tool is developed in the R programming language, leveraging the robust and flexible capabilities of the ggplot2 library (Wickham 2009). The package’s design benefits from ggplot2’s declarative nature, which simplifies the addition of new geometries to {funkyheatmap}.

For user convenience and understanding, we have put together comprehensive documentation resources. These include function-level documentations, which explain how to use public functions, the meaning of function arguments, and their possible values. We also offer detailed, step-by-step vignettes to demonstrate the range of customizations that {funkyheatmap} offers.

To ensure the continued quality and reliability of the package, we use the testthat framework for software testing, coupled with continuous integration practices. This combination provides us with a reliable system to catch any potential issues early and maintain the high quality of the software.

We used Viash (Cannoodt et al. 2021) to generate a CLI tool and Nextflow module to allow rendering funky heatmaps from CSV files (See the documentation site for more information).

Recognizing the wide usage of Python in data analysis, we have also developed a Python version of the package, funkyheatmappy. This package utilises the widely used matplotlib library (Hunter 2007) for its operations. To maintain consistency between the R and Python versions, we use shared test data across the implementations. This practice ensures that the visualisations produced by both versions are identical.

Lastly, to cater to the increasing demand for interactive data exploration, we are developing funkyheatmapjs, a JavaScript version of the tool. This interactive version will provide additional features such as sorting rows by clicking on a column and displaying labels on hover. These developments reinforce our commitment to continuous improvement and meeting the diverse needs of our user base.


The {funkyheatmap} package fills an important gap in the data visualisation landscape, addressing the need for visualising semantically mixed data types in an intuitive and comprehensive manner. With its user-friendly interface and extensive customization options, it provides a solution that is as accessible to novices as it is to experienced data scientists. It has already demonstrated its value across numerous benchmarking studies in the single-cell omics field, yet its potential applications extend to any field where these mixed data types need to be visualised.

The future is promising for {funkyheatmap}, with plans for continued enhancements and expansion of its capabilities. The Python package funkyheatmappy offers accessibility to Python-based workflows, while the ongoing development of the JavaScript port funkyheatmapjs, promises interactive exploration capabilities.


L.Z. acknowledges support from the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells). L.D. acknowledges support from the Research Foundation - Flanders (FWO) [1SF3822N].


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