adegenet: compoplot – R documentation

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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 class '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 class 'dapc'
compoplot(x, only.grp = NULL, border = NA, ...)

## S3 method for class '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

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

Author(s)

Thibaut Jombart thibautjombart@gmail.com

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release