colorSymbol: Color in ChemoSpec and ChemoSpec2D

In ChemoSpecUtils: Functions Supporting Packages ChemoSpec and ChemoSpec2D

Color in ChemoSpec and ChemoSpec2D

Description

In ChemoSpec and ChemoSpec2D, the user may use any color name/format known to R. The current color scheme of a Spectra or Spectra2D object may be determined using sumGroups or sumSpectra. The colors can also be queried and changed using conColScheme.

Format

Colors are stored as character vectors and symbols as numeric vectors.

Details

An important fact to keep in mind is that most people with normal vision cannot distinguish more than about 8-12 colors, and doing so depends upon the viewing circumstances: if on paper, printer, ink and paper type all matter, and if on a screen, the background color makes a big difference. Further, color-blind individuals have additional challenges. A great discussion of color issues can be found in the colorspace package. The Polychrome package has further discussion and utilities for choosing qualitative colorschemes, including those for color-blind individuals.

ChemoSpec, but not ChemoSpec2D, can also create plots using the built-in symbols and lower case letters. This is useful for color-blind individuals, plots in rgl which can't plot regular symbols, and plots for where there are more groups than could be reasonably coded in color. A good discussion of which symbols are most readily distinguished can be found in Robinson: "Good Plot Symbols by Default" Journal of Computational and Graphical Statistics DOI: 10.1080/10618600.2019.1637746

ChemoSpecUtils supplies four color/symbol schemes for your consideration. If the particular order of colors in any of these does not suit your needs, you can always choose the ones you want, and/or rearrange the order, or simply provide your own.

• The colors and symbols produced by gr.cols = "auto" in the import functions.

• Col8 provides eight unique colors. These are more saturated than the automatic colors.

• Col12 provides a mostly paired set of 12 unique colors suitable for groups that come in pairs.

• Col7 provides seven color-blind friendly colors. These can be visualized at https://projects.susielu.com/viz-palette by using the hex codes obtained by typing data(Col7); Col7 in the R console.

Author(s)

Bryan A. Hanson (DePauw University).

Examples

# Make a plot showing all the built-in color options

data(Col7)
data(Col12)
data(Sym12)
data(Col8)
data(Sym8)
# You need to install package "RColorBrewer" to display the default color scheme
if (requireNamespace("RColorBrewer", quietly = TRUE)) {
  auto <- RColorBrewer::brewer.pal(8, "Set1")
}

sp <- 0.75 # space between major plot elements
tsp <- 0.15 # additional space between points and color swatches/descriptive text
h <- 0.25 # height of the swatch
y <- 0.0 # bottom of the plot, the reference point

# empty plot
plot(1:12, rep(0.0, 12),
  type = "n", yaxt = "n", xaxt = "n", bty = "n",
  xlab = "", ylab = "", ylim = c(0, 3.5)
)
text(6.5, y + h + tsp * 4 + sp * 3.5,
  labels = "Automatic Color & Symbol Options", cex = 1.25, font = 2
)

# Col12
for (i in 1:12) {
  rect(i - 0.5, y, i + 0.5, y + h, border = NA, col = Col12[i])
}
points(1:12, rep(y + h + tsp, 12), pch = Sym12)
text(0.6, y + h + tsp * 2, adj = 0,
  labels = "gr.cols = 'Col12'     12 mostly paired distinct colors/symbols"
)

# Col8
for (i in 1:8) {
  rect(i - 0.5, y + sp, i + 0.5, y + sp + h, border = NA, col = Col8[i])
}
points(1:8, rep(y + h + tsp + sp, 8), pch = Sym8)
text(0.6, y + h + tsp * 2 + sp, adj = 0,
  labels = "gr.cols = 'Col8'     8 distinct colors/symbols"
)

# auto (default)
if (requireNamespace("RColorBrewer", quietly = TRUE)) {
  for (i in 1:8) {
    rect(i - 0.5, y + sp * 2, i + 0.5, y + sp * 2 + h, border = NA, col = auto[i])
  }
  points(1:8, rep(y + h + tsp + sp * 2, 8), pch = Sym8)
  text(0.6, y + h + tsp * 2 + sp * 2, adj = 0,
    labels = "gr.cols = 'auto'     8 distinct colors/symbols"
  )
}

# colorblind-friendly
for (i in 1:7) {
  rect(i - 0.5, y + sp * 3, i + 0.5, y + sp * 3 + h, border = NA, col = Col7[i])
}
points(1:7, rep(y + h + tsp + sp * 3, 7), pch = Sym8[1:7])
text(0.6, y + h + tsp * 2 + sp * 3, adj = 0,
  labels = "gr.cols = 'Col7'     7 colorblind-friendly colors"
)

ChemoSpecUtils documentation built on April 12, 2025, 5:07 p.m.