Generating colorblind-friendly scatter plots for single-cell data

Abstract
Data availability
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Abstract

Reduced-dimension or spatial in situ scatter plots are widely employed in bioinformatics papers analyzing single-cell data to present phenomena or cell-conditions of interest in cell groups. When displaying these cell groups, color is frequently the only graphical cue used to differentiate them. However, as the complexity of the information presented in these visualizations increases, the usefulness of color as the only visual cue declines, especially for the sizable readership with color-vision deficiencies (CVDs). In this paper, we present scatterHatch, an R package that creates easily interpretable scatter plots by redundant coding of cell groups using colors as well as patterns. We give examples to demonstrate how the scatterHatch plots are more accessible than simple scatter plots when simulated for various types of CVDs.

Data availability

The current manuscript is a computational study, so no new data have been generated for this manuscript. The scripts used for generating the figures in this manuscript are available at https://github.com/FertigLab/scatterHatch-paper.

The following previously published data sets were used

1. Lin et al
(2018) Single-cell intensity data used in Figures 7 and 8.
https://doi.org/10.7554/eLife.31657.024.

https://elifesciences.org/articles/31657#content

Article and author information

Author details

Tejas Guha

Department of Electrical and Computer Engineering, University of Maryland, College Park, College Park, United States

Competing interests
No competing interests declared.
Elana J Fertig

Department of Oncology, Johns Hopkins University, Baltimore, United States

For correspondence
ejfertig@jhmi.edu

Competing interests
Elana J Fertig, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0003-3204-342X
Atul Deshpande

Department of Oncology, Johns Hopkins University, Baltimore, United States

For correspondence
adeshpande@jhu.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-5144-6924

Funding

National Cancer Institute (U01CA253403)

Elana J Fertig

National Cancer Institute (U01CA212007)

Elana J Fertig

National Cancer Institute (P01CA247886)

Elana J Fertig

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.