PlotRelPairs {sequoia}

Plot Pairwise Relationships

Description

Plot pairwise 1st and 2nd degree relationships between individuals, similar to Colony's dyad plot.

Usage

PlotRelPairs(
  RelM = NULL,
  subset.x = NULL,
  subset.y = NULL,
  drop.U = TRUE,
  pch.symbols = FALSE,
  cex.axis = 0.7,
  mar = c(5, 5, 1, 8)
)

Arguments

RelM

square matrix with relationships between all pairs of individuals, as generated by GetRelM. Row and column names should be individual IDs.

subset.x

vector with IDs to show on the x-axis; the y-axis will include all siblings, parents and grandparents of these individuals.

subset.y

vector with IDs to show on the y-axis; the x-axis will include all siblings, offspring and grandoffspring of these individuals. Specify either subset.x or subset.y (or neither), not both.

drop.U

logical: omit individuals without relatives from the plot, and omit individuals without parents from the x-axis. Ignored if subset.x or subset.y is specified.

pch.symbols

logical: use different symbols for the different relationships (TRUE) or only colours in a heatmap-like fashion (FALSE). Question marks in the plot indicate that one or more of the symbols are not supported on your machine.

cex.axis

the magnification to be used for axis annotation. Decrease this value if R is dropping axis labels to prevent them from overlapping.

mar

A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.

Details

Parents are shown above the diagonal (y-axis is parent of x-axis), siblings below the diagonal. If present, grandparents and full aunts/uncles are also shown above the diagonal. Individuals are sorted by dam ID and sire ID so that siblings are grouped together, and then by generation (getGenerations) so that later generations are closer to the origin.

If RelM is based on a dataframe with pairs rather than a pedigree, parents and grandparents are similarly only displayed above the diagonal, but the order of individuals is arbitrary and the ID on the x-axis is as likely to be the grandparent of the one on the y-axis as vice versa. Second degree relatives of unknown classification ('2nd', may be HS, GP or FA) are only shown below the diagonal. The switch between pedigree-based versus pairs-based is made on whether parent-offspring pairs are coded as 'M','P', 'MP', 'O' (unidirectional, from pedigree) or as 'PO' (bidirectional, from pairs).

Note that half-avuncular and (double) full cousin pairs are ignored.

Value

The subsetted, rearranged RelM is returned invisible.

The numbers of unique pairs of each relationship type are given in the figure legend. The number of 'self' pairs refers to the number of individuals on the x-axis, not all of whom may occur on the y-axis when drop.U=TRUE or a subset is specified.

See Also

GetRelM; SummarySeq for individual-wise graphical pedigree summaries.

Examples

Rel.griffin <- GetRelM(Ped_griffin, patmat=TRUE, GenBack=2)
PlotRelPairs(Rel.griffin)

## Not run: 
PlotRelPairs(Rel.griffin, pch.symbols = TRUE)
# plot with unicode symbols not supported on all platforms

## End(Not run)

# parents & grandparents of 2008 cohort:
PlotRelPairs(Rel.griffin,
             subset.x = Ped_griffin$id[Ped_griffin$birthyear ==2008])
# offspring & grand-offspring of 2002 cohort:
PlotRelPairs(Rel.griffin,
             subset.y = Ped_griffin$id[Ped_griffin$birthyear ==2002])