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 'summary.loci': plot(x, loci, what = "both", layout = 1, col = c("blue", "red"), ...)
x, object |
an object of class "loci" or "genind" ,
a data frame, a factor, or a vector. |
details |
a logical value: if TRUE the data are printed as
a data frame; the default is FALSE . |
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 the barplots. |
... |
further arguments to be passed to or from other methods. |
Genotypes not observed in the data frame are not counted.
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