MetabolomicsBasics (version 1.4.5)

AdjustSymbols: AdjustSymbols.

Description

AdjustSymbols will generate plotting character and color vectors based on experimental factors.#'

Usage

AdjustSymbols(cols = NULL, pchs = NULL, colorset = NULL, symbolset = NULL)

Value

Either a vector (if one parameter of `cols` and `pchs` remains NULL), a data frame with columns `cols` and `pchs` (if both are provided and of equal length) or a list of length 2 (if both are provided and of different length). Will be used by several plotting functions of the package internally.

Arguments

cols

Factor (color output) or numeric (grey-scale output) vector or NULL (omitted).

pchs

Factor vector or NULL (omitted).

colorset

Color definitions for the factor levels of `cols` (can be omitted to use default values).

symbolset

Plotting character definitions for the factor levels of `pchs` (can be omitted to use default values).

Details

Using a fixed color and symbol scheme indicating samples from different groups throughout all figures of a analysis workflow is a reasonable decision. This function allows to specify both and attach it to a sample table for further use.

Examples

# return color vector
x <- gl(6, 3)
y <- as.numeric(x)
plot(y, bg = AdjustSymbols(cols = x), pch = 21, cex = 2)
plot(y, bg = AdjustSymbols(cols = y), pch = 21, cex = 2)
plot(y, bg = AdjustSymbols(cols = x, colorset = 1:6), pch = 21, cex = 2)
plot(y, pch = AdjustSymbols(pchs = x), cex = 2)
plot(y, bg = 2, pch = AdjustSymbols(pchs = x, symbolset = 1:6), cex = 2)

# load data and plot using provided color scheme
raw <- MetabolomicsBasics::raw
sam <- MetabolomicsBasics::sam
head(sam)
plot(y = raw[, 1], x = as.numeric(sam$GT), pch = sam$pchs, bg = sam$cols)

# change colors to greyscale
head(AdjustSymbols(cols = sam$GT, pchs = sam$Origin))
tmp.set <- grDevices::rainbow(length(levels(sam$GT)))
head(AdjustSymbols(cols = sam$GT, pchs = sam$Batch, colorset = tmp.set))
plot(raw[, 1] ~ sam$GT, col = unique_labels(sam = sam, g = "GT")[, "cols"])
sam$cols <- AdjustSymbols(cols = as.numeric(sam$GT))
plot(raw[, 1] ~ sam$GT, col = unique_labels(sam = sam, g = "GT")[, "cols"]) #'