Create plotting data frame from a Pedigree

Convert a Pedigree to a data frame with all the elements and their characteristic for them to be plotted afterwards with plot_fromdf().

Usage

# S4 method for class 'Pedigree'
ped_to_plotdf(
  obj,
  packed = TRUE,
  width = 6,
  align = c(1.5, 2),
  align_parents = TRUE,
  force = FALSE,
  cex = 1,
  symbolsize = cex,
  pconnect = 0.5,
  branch = 0.6,
  aff_mark = TRUE,
  id_lab = "id",
  label = NULL,
  precision = 4,
  lwd = par("lwd"),
  tips = NULL,
  ...
)

Arguments

obj

A Pedigree object

...

Other arguments passed to par()

packed

Should the Pedigree be compressed. (i.e. allow diagonal lines connecting parents to children in order to have a smaller overall width for the plot.)

width

For a packed output, the minimum width of the plot, in inches.

align

For a packed Pedigree, align children under parents TRUE, to the extent possible given the page width, or align to to the left margin FALSE. This argument can be a two element vector, giving the alignment parameters, or a logical value. If TRUE, the default is c(1.5, 2), or if numeric the routine alignped4() will be called.

align_parents

If align_parents = TRUE, go one step further and try to make both parents of each child have the same depth. (This is not always possible). It helps the drawing program by lining up pedigrees that 'join in the middle' via a marriage.

force

If force = TRUE, the function will return the depth minus min(depth) if depth reach a state with no founders is not possible.

cex

Character expansion of the text

symbolsize

Size of the symbols

pconnect

When connecting parent to children the program will try to make the connecting line as close to vertical as possible, subject to it lying inside the endpoints of the line that connects the children by at least pconnect people. Setting this option to a large number will force the line to connect at the midpoint of the children.

branch

defines how much angle is used to connect various levels of nuclear families.

aff_mark

If TRUE, add a aff_mark to each box corresponding to the value of the affection column for each filling scale.

id_lab

The column name of the id for each individuals.

label

If not NULL, add a label to each box under the id corresponding to the value of the column given.

precision

The number of significatif numbers to round the solution to.

lwd

default=par("lwd"). Controls the line width of the segments, arcs and polygons.

tips

A character vector of the column names of the data frame to use as tooltips. If NULL, no tooltips are added.

Value

A list containing the data frame and the user coordinates.

Details

The data frame contains the following columns:

• x0, y0, x1, y1: coordinates of the elements

• type: type of the elements

• fill: fill color of the elements

• border: border color of the elements

• angle: angle of the shading of the elements

• density: density of the shading of the elements

• cex: size of the elements

• label: label of the elements

• tips: tips of the elements (used for the tooltips)

• adjx: horizontal text adjustment of the labels

• adjy: vertical text adjustment of the labels

All those columns are used by plot_fromdf() to plot the graph.

See also

plot_fromdf() ped_to_legdf()

Examples

data(sampleped)
ped1 <- Pedigree(sampleped[sampleped$famid == 1,])
plot_df <- ped_to_plotdf(ped1)
summary(plot_df$df)
#>       id                  x0                y0              x1         
#>  Length:262         Min.   :-0.6265   Min.   :1.000   Min.   :-0.6265  
#>  Class :character   1st Qu.: 3.0000   1st Qu.:2.602   1st Qu.: 3.0000  
#>  Mode  :character   Median : 6.5100   Median :3.092   Median : 7.0050  
#>                     Mean   : 6.9442   Mean   :3.133   Mean   : 7.0476  
#>                     3rd Qu.:11.0100   3rd Qu.:4.000   3rd Qu.:11.0025  
#>                     Max.   :15.0100   Max.   :4.454   Max.   :15.0100  
#>                                                       NA's   :146      
#>        y1             type               fill              border         
#>  Min.   :0.9815   Length:262         Length:262         Length:262        
#>  1st Qu.:2.7008   Class :character   Class :character   Class :character  
#>  Median :3.0920   Mode  :character   Mode  :character   Mode  :character  
#>  Mean   :2.9837                                                           
#>  3rd Qu.:3.6023                                                           
#>  Max.   :4.2400                                                           
#>  NA's   :146                                                              
#>      angle        density         cex           label          
#>  Min.   : NA   Min.   : NA   Min.   :0.700   Length:262        
#>  1st Qu.: NA   1st Qu.: NA   1st Qu.:1.000   Class :character  
#>  Median : NA   Median : NA   Median :1.000   Mode  :character  
#>  Mean   :NaN   Mean   :NaN   Mean   :1.015                     
#>  3rd Qu.: NA   3rd Qu.: NA   3rd Qu.:1.000                     
#>  Max.   : NA   Max.   : NA   Max.   :2.500                     
#>  NA's   :262   NA's   :262                                     
#>      tips                adjx          adjy             lty     
#>  Length:262         Min.   :0.5   Min.   :0.5000   Min.   :19   
#>  Class :character   1st Qu.:0.5   1st Qu.:0.5000   1st Qu.:19   
#>  Mode  :character   Median :0.5   Median :1.0000   Median :19   
#>                     Mean   :0.5   Mean   :0.7647   Mean   :19   
#>                     3rd Qu.:0.5   3rd Qu.:1.0000   3rd Qu.:19   
#>                     Max.   :0.5   Max.   :1.0000   Max.   :19   
#>                     NA's   :160   NA's   :160      NA's   :260  
plot_fromdf(plot_df$df, usr = plot_df$par_usr$usr,
    boxh = plot_df$par_usr$boxh, boxw = plot_df$par_usr$boxw
)