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 = 3,
  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 decimal places 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.

Examples


data(sampleped)
ped1 <- Pedigree(sampleped[sampleped$famid == 1,])
plot_df <- ped_to_plotdf(ped1)
summary(plot_df$df)
#>       id                  x0               y0              x1        
#>  Length:212         Min.   : 0.000   Min.   :1.000   Min.   : 0.000  
#>  Class :character   1st Qu.: 3.000   1st Qu.:2.487   1st Qu.: 3.331  
#>  Mode  :character   Median : 7.000   Median :3.093   Median : 7.505  
#>                     Mean   : 7.296   Mean   :3.089   Mean   : 7.641  
#>                     3rd Qu.:11.750   3rd Qu.:4.000   3rd Qu.:11.831  
#>                     Max.   :15.010   Max.   :4.264   Max.   :15.010  
#>                                                      NA's   :126     
#>        y1            type               fill              border         
#>  Min.   :1.093   Length:212         Length:212         Length:212        
#>  1st Qu.:2.356   Class :character   Class :character   Class :character  
#>  Median :2.750   Mode  :character   Mode  :character   Mode  :character  
#>  Mean   :2.876                                                           
#>  3rd Qu.:3.553                                                           
#>  Max.   :3.750                                                           
#>  NA's   :126                                                             
#>      angle        density         cex       label               tips          
#>  Min.   : NA   Min.   : NA   Min.   :1   Length:212         Length:212        
#>  1st Qu.: NA   1st Qu.: NA   1st Qu.:1   Class :character   Class :character  
#>  Median : NA   Median : NA   Median :1   Mode  :character   Mode  :character  
#>  Mean   :NaN   Mean   :NaN   Mean   :1                                        
#>  3rd Qu.: NA   3rd Qu.: NA   3rd Qu.:1                                        
#>  Max.   : NA   Max.   : NA   Max.   :1                                        
#>  NA's   :212   NA's   :212                                                    
#>       adjx          adjy     
#>  Min.   :0.5   Min.   :0.50  
#>  1st Qu.:0.5   1st Qu.:0.50  
#>  Median :0.5   Median :0.75  
#>  Mean   :0.5   Mean   :0.75  
#>  3rd Qu.:0.5   3rd Qu.:1.00  
#>  Max.   :0.5   Max.   :1.00  
#>  NA's   :128   NA's   :128   
plot_fromdf(plot_df$df, usr = plot_df$par_usr$usr,
    boxh = plot_df$par_usr$boxh, boxw = plot_df$par_usr$boxw
)

Usage

Arguments

Value

Details

See also

Examples