Description Usage Arguments Value Methods (by class) Examples
Given an IBD matrix or a list of matrices, a graphical genotype plot is returned. Graphical genotypes allow to assess which homologue an individual has obtained, they highlight putative errors and show noninformative genotypes.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  graphical_genotype(
IBD,
only_informative = F,
cex.axis = 0.8,
main = NULL,
non_inf = c(0.3, 0.7),
...
)
## S3 method for class 'matrix'
graphical_genotype(
IBD,
only_informative = F,
cex.axis = 0.8,
main = NULL,
non_inf = c(0.3, 0.7),
...
)
## S3 method for class 'list'
graphical_genotype(
IBD,
only_informative = F,
cex.axis = 0.8,
main = NULL,
non_inf = c(0.3, 0.7),
...
)

IBD 
IBD matrix or list of IBD matrices. If IBD is a list, the names are used as subplot titles. 
only_informative 
logical, should only informative markers be plotted? False by default. 
cex.axis 
size of the bottom labels. 
main 
title to display in the plot. 
non_inf 
numeric, lower and upper probability boundaries to consider an IBD probability noninformative (if they fall within the threshold they will be ignored during prediction). Defaults to 0.3  0.7. Symmetrical boundaries are recommended but not necessary. 
... 
Additional parameters to be passed to 'plot'. For instance 'cex.axis' or 'main'. 
A plot containing graphical representations of IBD. Dark is a probability close to 1 and light is a probability close to 0.
matrix
: function for a single matrix.
list
: function for a list of matrices.
1 2 3 4 5 6 7  data("smooth_descent")
IBD < sdescent$predIBD
#One single homologue
graphical_genotype(IBD[[1]], only_informative = TRUE)
#Or all homologues
graphical_genotype(IBD, only_informative = TRUE)

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