Generating colorblind-friendly scatter plots for single-cell data
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Curated by eLife
eLife assessment
This manuscript is extremely useful for describing an R package that provides a valuable pattern and overlay framework for producing colorblind-friendly scatter plots for the field. The utility of this tool for making plots more accessible was demonstrated compellingly. This work will be of broad interest to many biomedical scientists, especially to viewers with color-vision deficiency.
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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.
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eLife assessment
This manuscript is extremely useful for describing an R package that provides a valuable pattern and overlay framework for producing colorblind-friendly scatter plots for the field. The utility of this tool for making plots more accessible was demonstrated compellingly. This work will be of broad interest to many biomedical scientists, especially to viewers with color-vision deficiency.
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Reviewer #1 (Public Review):
This is a relatively straightforward manuscript describing an r package that attempts to address issues in color-blindness in the interpretation of multicolor overlapping plots. The demonstration of its usefulness is solid and the findings will be significant in that they should become one of the standards that the scientific community strives to achieve for greater inclusiveness.
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Reviewer #2 (Public Review):
The authors present an R/Bioconductor package, scatterHatch, aimed at providing a novel framework for the creation of color-vision deficiency (CVD) accessible plots. The authors lay out that in increasingly common dimensionality reduction plots, like UMAPs and tSNEs, color tends to be the primary factor for distinguishing points of distinct groups. Although color palettes created with accessibility to CVDs in mind are often helpful, none adequately cater to all forms of CVD. Further, when too many colors are needed, even viewers with full-color vision may struggle. The authors lay out the current primary alternative to color, using point shape, which only works for sparse plotting regions, but most data points in UMAP and tSNE plots are not in sparse regions of the plot. All very true, thus demonstrating the …
Reviewer #2 (Public Review):
The authors present an R/Bioconductor package, scatterHatch, aimed at providing a novel framework for the creation of color-vision deficiency (CVD) accessible plots. The authors lay out that in increasingly common dimensionality reduction plots, like UMAPs and tSNEs, color tends to be the primary factor for distinguishing points of distinct groups. Although color palettes created with accessibility to CVDs in mind are often helpful, none adequately cater to all forms of CVD. Further, when too many colors are needed, even viewers with full-color vision may struggle. The authors lay out the current primary alternative to color, using point shape, which only works for sparse plotting regions, but most data points in UMAP and tSNE plots are not in sparse regions of the plot. All very true, thus demonstrating the need for a tool like scatterHatch, which can overlay hatch patterns both over regions in dense portions of a scatter plot, and also over points within automatically detected sparsely populated regions. The primary function of scatterHatch produces such plots from a given data frame and the names of columns to use for x, y, and color. The authors go on to demonstrate, with example figures, how the hatch patterns are indeed helpful in cases where color is not enough on its own. They demonstrate that the user can delineate custom hatch patterns, which gives flexibility to the user over how much to rely on hatch patterns versus color. Of particular note, the authors show how scatterHatch can be helpful for readers with monochromatic vision, a population that other visualization tools designed with CVD-accessibility in mind often still fail to aid.
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