R: Genotype composition plot

compoplot {adegenet} | R Documentation

## 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

[Package adegenet version 2.1.4 Index]