AdjustSymbols: AdjustSymbols.

In MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices

AdjustSymbols.

Description

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

Usage

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

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.

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.

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"]) #'

MetabolomicsBasics documentation built on Nov. 2, 2023, 5:07 p.m.