Background: Color Vision Deficiency (CVD), commonly known as colorblindness, affects approximately 300 million people worldwide. Individuals with CVD do not experience complete loss of color vision, but have reduced ability to distinguish different colors. When creating scientific figures, it is important to consider that individuals with CVD may not perceive all colors as intended. While there are several CVD friendly color palettes available, they are often insufficient for visualizing complex data that is often generated in microbiome studies. Methods: To overcome CVD accessibility for microbiome datasets, we developed an R package, microshades. Microshades includes CVD accessible color palettes and data organization functions. To construct the palettes, hue (type of color), chroma (colorfulness), and luminance (brightness) were adjusted for optimal visual distinction and CVD accessibility. All shades were tested with a CVD simulator (cvdemulator) for accessibility. In addition to accessible color palettes, we also provide data organization functions. These include grouping data by taxonomic ranking, sorting the data vertically and horizontally, and restructuring the plot legends. Results: Each microshades color palette contains six hues with five sequential variations of chroma and luminance per hue, for a total of 30 available colors per palette. The microshades_cvd_palettes colors are universally CVD accessible to individuals with the three most common types of CVD (Deuteranope, Protanope, and Tritanope). The individual hues of the microshades_palettes colors are CVD friendly, but when used in conjunction with multiple hues, may not be universally accessible to all forms of CVD. Discussion: The microshades R package is a visualization tool designed for microbiome researchers. The package contains two CVD accessible palettes, along with several organization features. The microshades package can be used in conjunction with common microbiome R packages, such as phyloseq, to enhance microbiome data visualization.

Link to paper: https://journals.asm.org/doi/10.1128/mra.00795-22