compoplot | R Documentation |
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:
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, ...)
x |
an object to be used for plotting (see description) |
... |
further arguments to be passed to |
col.pal |
a color palette to be used for the groups; defaults to |
border |
a color for the border of the barplot; use |
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 |
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
Thibaut Jombart thibautjombart@gmail.com
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