R package for creating publication-ready bubble heatmaps.
ggseabubble exploits gpplot2 and patchwork to create a heatmap-like visualization inspired by Bubble GUM (Spinelli, L. et al., 2015) that allows to sumarize several GSEA comparisons in a single plot.
A bubble heatmap represents comparisons as columns and signatures as rows. The colour of the bubble is proportional to the NES and the size of the bubble to the FDR-adjusted p-value. Empty bubbles represent non-significant results. Rows and columns can be clustered according to the distance between NES.
The ggseabubble package is implemented in R >= 4.0.0. We recommend running the installation via mamba:
# Create a conda environment.
conda create -n ggseabubble
# Activate the environment.
conda activate ggseabubble
# Install beyondcell package and dependencies.
mamba install -c mjjimenez r-ggseabubbleMaría José Jiménez-Santos
If you use ggseabubble in your work, please cite us:
Jimenez-Santos MJ. ggseabubble: R package for creating publication-ready bubble heatmaps. Version 1.0.0. 2023. doi:10.5281/zenodo.10692491.
If you have any questions regarding the use of ggseabubble, feel free to submit an issue.
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