R: Plot mean performances of assemblages that contain a given...

plot_components_box

R Documentation

Plot mean performances of assemblages that contain a given component

Description

Plot performances of assemblages that contain a given component as boxplots, possibly horizontally or vertically, by decreasing or increasing values or in the same order as the tree clustering.

Usage

plot_components_box(fobs, mOccur, sres,
                    ordre = NULL, ylim = range(fobs),
                    elt.wdw = seq_len(dim(mOccur)[2]),
                    main     = "",
                    pvalue   = fpvalue(),
                    opt.mean = "amean", opt.hor = TRUE  )

Arguments

`fobs`	a numeric vector. The vector `fobs` contains the quantitative performances of assemblages.
`mOccur`	a matrix of occurrence (occurrence of elements). Its first dimension equals to `length(fobs)`. Its second dimension equals to the number of elements.
`sres`	a table generated by the function `sort_motifs`. The table contains statistical properties of assembly motifs, sorted by increasing or decreasing mean performances.
`ordre`	an integer vector of `length(fobs)`. The vector contains labels for each assemblages, that determine the order for assembly motifs.
`ylim`	a vector of two numerics. The numerics are extrem values of performance `y-axis`.
`elt.wdw`	a vector of integers. It indicates the components to plot.
`main`	a string. The string is used as graph title.
`pvalue`	a probability, used as threshold in the variance analysis. Then `pvalue` must be higher than `0` and lower than `1`. Groups significantly different (at a p-value < `pvalue`) are then indicated by differents letters on the right of boxplots.
`opt.mean`	a character equals to `"amean"` or `"gmean"`. Switch to arithmetic formula if `opt.mean = "amean"`. Switch to geometric formula if `opt.mean = "gmean"`.
`opt.hor`	a logical. If `opt.hor = TRUE`, boxplot is plotted as horizontal boxes alongside a vertical y-axis of performances. If `opt.hor = FALSE`, boxplot is plotted as vertical boxes alongside a horizontal y-axis of performances.

Details

None.

Value

Nothing. It is a procedure.