Plot a Mass Isotopomer Distribution (MID) for multiple samples.

plotMID will plot Mass Isotopomer Distributions (MIDs).

Usage

plotMID(
  mid = NULL,
  gr = NULL,
  name = "unknown",
  contr = NULL,
  stackedbars = FALSE,
  subplot_ylim = 100,
  ...
)

Arguments

mid: Matrix of corrected MIDs. Samples in columns, MID values in rows.
gr: Groups, a factor vector of length ncol(mid).
name: Name of analyte for annotation.
contr: Contrasts. Not yet clear if useful.
stackedbars: Alternative plotting layout using stacked bar plot.
subplot_ylim: Calculate `ylim` individually per subplot if 0, show full range in all subplots if 100 and limit to the minimal specified number otherwise.
...: Further arguments to 'boxplot' or 'barplot' (depending on parameter 'stackedbars').

Value

An annotated barplot or boxplot.

Details

Multiple styling options are available using the function parameters.

Examples

mid <- matrix(c(seq(0, 0.3, 0.1), seq(1, 0.7, -0.1)), byrow = TRUE, nrow = 2)
gr <- gl(2, 2, labels = letters[1:2])
plotMID(mid = mid, gr = gr, name = "Metabolite X")

plotMID(mid = mid, gr = gr, stackedbars = TRUE, las = 1, xlab = "MID")

lt <- paste0("M", 0:1)
rownames(mid) <- lt
plotMID(mid = mid, gr = gr, stackedbars = TRUE, xlab = "MID", legend.text = lt)

plotMID(mid = mid[, 2, drop = FALSE], stackedbars = TRUE, col = c(3, 4))

colnames(mid) <- paste0("S", 1:4)
gr2 <- gl(n = 1, k = 1, labels = "bla")
plotMID(mid = mid[, 2, drop = FALSE], gr = gr2, stackedbars = TRUE, name = NULL)

plotMID(mid = mid, gr = factor(colnames(mid)), stackedbars = TRUE, name = NULL)