summary.loci {pegas} | R Documentation |
These functions print and summarize table of alleles and loci (objects
of class "loci"
).
## S3 method for class 'loci': print(x, details = FALSE, ...) ## S3 method for class 'loci': summary(object, ...) ## S3 method for class 'summary.loci': print(x, ...) ## S3 method for class 'loci': x[i, j, drop = TRUE] ## S3 method for class 'summary.loci': plot(x, loci, what = "both", layout = 1, col = c("blue", "red"), ...)
x, object |
an object of class "loci" or "summary.loci" . |
details |
a logical value: if TRUE the data are printed as
a data frame; the default is FALSE . |
i, j |
indices of the rows and/or columns to select or to drop. They may be numeric, logical, or character (in the same way than for standard R objects). |
drop |
a logical specifying whether to returned an object of
the smallest dimension possible, i.e., may return a vector or a
factor if drop = TRUE . |
loci |
the loci (genes) to be plotted. By default, all loci are plotted. |
what |
the frequencies to be plotted. Three choices are possible:
"alleles" , "genotypes" , and "both" (the default),
or any unambiguous abbreviations. |
layout |
the number of graphs to be plotted simultaneously. |
col |
the colours used for the barplots. |
... |
further arguments to be passed to or from other methods. |
Genotypes not observed in the data frame are not counted.
When using the [
method, if only one column is extracted or if
the returned data frame has no `loci' column, then the class
"loci"
is dropped.
An object of class "loci"
can be edited in the R data editor
with, e.g., fix(x)
or x <- edit(x)
.
summary.loci
returns a list with the genes as names and each
element made a list with two vectors "genotype"
and
"allele"
with the frequencies (numbers) of genotypes and
alleles, respectively. The names of these two vectors are the observed
genotypes and alleles.
print
and plot
methods return NULL.
Emmanuel Paradis
read.loci
, getAlleles
, edit.loci
require(adegenet) data(nancycats) x <- as.loci(nancycats) s <- summary(x) plot(s, layout=20, las=2) layout(1)