bplot: Karlin B plot
In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description Usage Arguments Value Examples

Plot distances of each gene's CU frequency to specified gene (sub)sets (given by x and y).

Bplot(x, y, data, annotations = character(), ribosomal = FALSE,
  reference = list(), size = 1, alpha = 0.5)

## S4 method for signature 'character,character,matrix'
Bplot(x, y, data,
  annotations = character(), ribosomal = FALSE, reference = list(),
  size = 1, alpha = 0.5)

## S4 method for signature 'numeric,numeric,missing'
Bplot(x, y, data,
  annotations = character(), ribosomal = FALSE, reference = list(),
  size = 1, alpha = 0.5)

`x, y`	Character, both must be in `colnames(data)`, or numeric vectors of CU statistic values for two subsets of genes. If numeric, the vectors must be of the same length.
`data`	A matrix with CU statistic values for subsets of genes in columns.
`annotations`	A character vector giving KO annotations for sequences for which the CU values were calculated, must be of length `nrow(data)`.
`ribosomal`	Logical, whether to indicate ribosomal genes in the plot. Default is `FALSE`, if set to `TRUE`, then `annotation` must be given.
`reference`	A named list of length 1, containing either a logical vector of `nrow(data)` of reference genes to be indicated on the plot, or a character vector (of any length) of the reference genes' anotations. If latter is the case, then `annotation` must be given.
`size`	Numeric, indicating points' size
`alpha`	Numeric, between 0 and 1, indicating points' transparency (default is 0.1).

A ggplot object.

require(ggplot2)

# calculate MILC distance to the average CU of the example DNA sequences,
# and to the average CU of ribosomal genes among the example DNA sequences
milc <- MILC(LD94, self = TRUE, ribosomal = TRUE)

Bplot(x = "ribosomal", y = "self", data = milc,
      ribosomal = TRUE, annotations = getKO(LD94),
      size = 3) +
    labs(x = "MILC distance to ribosomal genes",
         y = "MILC distance to genes' average CU")