compoplot: Genotype composition plot

Description

The compoplot uses a barplot to represent the group assignment probability of individuals to several groups. It is a generic with methods for the following objects:

Usage

compoplot(x, ...)
# S3 method for matrix
compoplot(
  x,
  col.pal = funky,
  border = NA,
  subset = NULL,
  show.lab = FALSE,
  lab = rownames(x),
  legend = TRUE,
  txt.leg = colnames(x),
  n.col = 4,
  posi = NULL,
  cleg = 0.8,
  bg = transp("white"),
  ...
)
# S3 method for dapc
compoplot(x, only.grp = NULL, border = NA, ...)
# S3 method for snapclust
compoplot(x, border = NA, ...)

Arguments

x: an object to be used for plotting (see description)
...: further arguments to be passed to barplot
col.pal: a color palette to be used for the groups; defaults to funky
border: a color for the border of the barplot; use NA to indicate no border.
subset: a subset of individuals to retain
show.lab: a logical indicating if individual labels should be displayed
lab: a vector of individual labels; if NULL, row.names of the matrix are used
legend: a logical indicating whether a legend should be provided for the colors
txt.leg: a character vector to be used for the legend
n.col: the number of columns to be used for the legend
posi: the position of the legend
cleg: a size factor for the legend
bg: the background to be used for the legend
only.grp: a subset of groups to retain

Author

Thibaut Jombart thibautjombart@gmail.com

Details

matrix: a matrix with individuals in row and genetic clusters in column, each entry being an assignment probability of the corresponding individual to the corresponding group
dapc: the output of the dapc function; in this case, group assignments are based upon geometric criteria in the discriminant space
snapclust: the output of the snapclust function; in this case, group assignments are based upon the likelihood of genotypes belonging to their groups