Applying SomaLogic Themes and Palettes • SomaPlotr

This vignette provides an overview of the color palettes, ggplot2 themes, and color scales available in SomaPlotr. These features can be used to generate colorful, polished, and visually consistent graphics.

The following packages will be required to run the code in this vignette natively:

library(SomaPlotr)
#> Registered S3 method overwritten by 'SomaPlotr':
#>   method   from      
#>   plot.Map SomaDataIO
library(ggplot2)
library(gridExtra)
library(withr)
library(scales)

Hexadecimal Color Lists

SomaPlotr provides lists that define hexadecimal codes for colors used in SomaLogic branding and marketing materials. A hexadecimal (hex) color is specified with the format #RRGGBB, where the red (RR), green (GG), and blue (BB) components of the color are hex values between 00 and FF. The hexadecimal color lists in SomaPlotr are designed to clearly distinguish groups and can be applied to a variety of graphics types, with options for both color and greyscale graphics.

Branding Colors

soma_colors is a list of hex values corresponding to 10 colors from the SomaLogic Operating Co. branding color scheme (prior to 2020), in darker and more subdued shades than what is used today.

# Display the hex color codes in the list
soma_colors
#> $purple
#> [1] "#24135F"
#> 
#> $lightgreen
#> [1] "#00A499"
#> 
#> $lightgrey
#> [1] "#707372"
#> 
#> $magenta
#> [1] "#840B55"
#> 
#> $lightblue
#> [1] "#006BA6"
#> 
#> $yellow
#> [1] "#D69A2D"
#> 
#> $darkgreen
#> [1] "#007A53"
#> 
#> $darkblue
#> [1] "#1B365D"
#> 
#> $darkgrey
#> [1] "#54585A"
#> 
#> $blue
#> [1] "#004C97"

# Show a preview of all list colors
scales::show_col(unlist(soma_colors))

soma_colors2 contains the exact colors (N = 8) used in current official SomaLogic branding materials, but contains fewer values than soma_colors:

soma_colors2
#> $blue
#> [1] "#4067E2"
#> 
#> $teal
#> [1] "#59CFDB"
#> 
#> $pink
#> [1] "#DB40EF"
#> 
#> $yellow
#> [1] "#FFAA0F"
#> 
#> $green
#> [1] "#2F9862"
#> 
#> $turq
#> [1] "#0B6975"
#> 
#> $lightblue
#> [1] "#0077E0"
#> 
#> $purple
#> [1] "#170BA5"
scales::show_col(unlist(soma_colors2))

Values from these color lists can be directly supplied to visualization utilities (like ggplot2) to designate colors for specific graphical elements:

# Provide color values for individual plot elements
ggplot(iris, aes(x = Species, y = Sepal.Width)) +
  geom_boxplot(fill = soma_colors2$teal,
               outlier.color = soma_colors2$yellow) +
  geom_jitter(color = soma_colors2$pink)

When coerced to a vector, the entire palette can be supplied as an argument to base R plotting utilities:

hist(iris$Sepal.Length, col = unlist(soma_colors))

Greys and Risk

SomaPlotr provides two additional lists of convenient color schemes for non-color or risk-stratified graphics. The first, soma_colors_greys, contains only greyscale values, and is best used for materials (e.g. printed documents) where color display is not guaranteed:

soma_colors_greys
#> $black
#> [1] "#000000"
#> 
#> $darkgrey2
#> [1] "#333333"
#> 
#> $darkgrey1
#> [1] "#444444"
#> 
#> $grey
#> [1] "#9DABB2"
#> 
#> $lightgrey2
#> [1] "#C4CDD1"
#> 
#> $lightgrey1
#> [1] "#EEF1F2"
scales::show_col(unlist(soma_colors_greys))

The second, soma_colors_risk, contains colors commonly used for risk designation:

soma_colors_risk
#> $red
#> [1] "#B33D26"
#> 
#> $orange
#> [1] "#D57800"
#> 
#> $yellow
#> [1] "#D9C756"
#> 
#> $green
#> [1] "#5CAA7F"
#> 
#> $blue
#> [1] "#004C97"
scales::show_col(unlist(soma_colors_risk))

Color Palettes Generator

The color lists described in the previous section contain a finite number of values. For graphics involving a large number of groups, these lists may not provide enough values for each group. The palette_soma() function remedies this by by recycling values from the soma_colors2 list, allowing the user to generate a hex color vector of N length.

# This list only contains 8 values
length(soma_colors2)
#> [1] 8

# This function can create a vector of any length
palette_soma(10)
#>  [1] "#4067E2" "#59CFDB" "#DB40EF" "#FFAA0F" "#2F9862" "#0B6975"
#>  [7] "#0077E0" "#170BA5" "#4067E2" "#59CFDB"

See below for visual displays of palette_soma() in action:

scales::show_col(palette_soma(5))


scales::show_col(palette_soma(10))

For example, in the simulated dataset below, there are 15 groups, but soma_colors2 only contains 8 values:

groups <- paste("Grp", seq(1, 15, 1L))
withr::with_seed(123, {
  n <- 200
  df <- data.frame(seq.1234.56 = rnorm(n, 2, 0.5),
                   Group = sample(groups, n, replace = TRUE)
                   )
})

We can use palette_soma() to recycle the soma_colors2 values and generate a hex vector of length 15. We can then use that vector to assign colors (using ggplot2::scale_fill_manual()) in a graphic containing boxplots:

pal <- palette_soma(length(groups))

ggplot(df, aes(x = Group, y = seq.1234.56, fill = Group)) +
  geom_boxplot() +
  scale_fill_manual(values = pal) +
  theme(legend.position = "none")

ggplot2 Themes & Scales

Theme

ggplot2 themes provide a method for easy customization of all non-data components of plots (e.g. titles, labels, fonts, background, grid lines, legends, and more). SomaPlotr uses themes to give plots a consistent look, as well as save time and effort when finalizing and polishing multiple plots. The theme_soma() theme applies a predetermined set of modifications to each plot for convenience and consistency. These include modifying the x- and y-axis labels, removing the (default) grey-filled background, moving the figure legend, and more:

# Default ggplot2 theme
default_plot <- gg$point
themeSoma_plot <- gg$point + theme_soma()

grid.arrange(default_plot, themeSoma_plot, ncol = 2)

Scales

SomaPlotr contains ggplot2-compatible scales, both continuous and discrete, that can be applied to previously generated plots. See below for examples.

gg$point + scale_color_soma()

gg$bar + scale_fill_soma()

gg$box + scale_fill_soma_risk()

Other scales include: