Scales object

A Scales object is a list of two data.frame. The first one is used to represent the affection status of the individuals and therefore the filling of the individuals in the pedigree plot. The second one is used to represent the availability status of the individuals and therefore the border color of the individuals in the pedigree plot.

Constructor :

You need to provide both fill and border in the dedicated parameters. However this is usually done using the generate_colors() function with a Pedigree object.

Usage

Scales(fill, border)

# S4 method for class 'data.frame,data.frame'
Scales(fill, border)

Arguments

fill

A data.frame with the informations for the affection status. The columns needed are:

'order': the order of the affection to be used
'column_values': name of the column containing the raw values in the Ped object
'column_mods': name of the column containing the mods of the transformed values in the Ped object
'mods': all the different mods
'labels': the corresponding labels of each mods
'affected': a logical value indicating if the mod correspond to an affected individuals
'fill': the color to use for this mods
'density': the density of the shading
'angle': the angle of the shading

border

A data.frame with the informations for the availability status. The columns needed are:

'column_values': name of the column containing the raw values in the Ped object
'column_mods': name of the column containing the mods of the transformed values in the Ped object
'mods': all the different mods
'labels': the corresponding labels of each mods
'border': the color to use for this mods

Value

A Scales object.

Slots

fill

A data.frame with the informations for the affection status. The columns needed are:

'order': the order of the affection to be used
'column_values': name of the column containing the raw values in the Ped object
'column_mods': name of the column containing the mods of the transformed values in the Ped object
'mods': all the different mods
'labels': the corresponding labels of each mods
'affected': a logical value indicating if the mod correspond to an affected individuals
'fill': the color to use for this mods
'density': the density of the shading
'angle': the angle of the shading

border

A data.frame with the informations for the availability status. The columns needed are:

'column_values': name of the column containing the raw values in the Ped object
'column_mods': name of the column containing the mods of the transformed values in the Ped object
'mods': all the different mods
'labels': the corresponding labels of each mods
'border': the color to use for this mods

Accessors

fill(x) : Get the fill data.frame

fill(x) <- value : Set the fill data.frame

border(x) : Get the border data.frame

border(x) <- value : Set the border data.frame from the Scales object.

Generics

as.list(x): Convert a Scales object to a list

Examples


Scales(
    fill = data.frame(
        order = 1,
        column_values = "affected",
        column_mods = "affected_mods",
        mods = c(0, 1),
        labels = c("unaffected", "affected"),
        affected = c(FALSE, TRUE),
        fill = c("white", "red"),
        density = c(NA, 20),
        angle = c(NA, 45)
    ),
    border = data.frame(
        column_values = "avail",
        column_mods = "avail_mods",
        mods = c(0, 1),
        labels = c("not available", "available"),
        border = c("black", "blue")
    )
)
#> An object of class "Scales"
#> Slot "fill":
#>   order column_values   column_mods mods     labels affected  fill density
#> 1     1      affected affected_mods    0 unaffected    FALSE white      NA
#> 2     1      affected affected_mods    1   affected     TRUE   red      20
#>   angle
#> 1    NA
#> 2    45
#> 
#> Slot "border":
#>   column_values column_mods mods        labels border
#> 1         avail  avail_mods    0 not available  black
#> 2         avail  avail_mods    1     available   blue
#>