Bplot {coRdon} | R Documentation |
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 |
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
|
ribosomal |
Logical, whether to indicate ribosomal genes in the plot.
Default is |
reference |
A named list of length 1, containing either a logical
vector of |
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")