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Process the filling and border colors based on affection and availability

Source: R/generate_colors.R
generate_colors.Rd

Perform transformation uppon a dataframe given to compute the colors for the filling and the border of the individuals based on the affection and availability status.

Usage

# S4 method for class 'character'
generate_colors(
  obj,
  avail,
  mods_aff = NULL,
  is_num = FALSE,
  keep_full_scale = FALSE,
  colors_aff = c("yellow2", "red"),
  colors_unaff = c("white", "steelblue4"),
  colors_avail = c("green", "black"),
  colors_na = "grey"
)

# S4 method for class 'numeric'
generate_colors(
  obj,
  avail,
  threshold = 0.5,
  sup_thres_aff = TRUE,
  is_num = TRUE,
  keep_full_scale = FALSE,
  breaks = 3,
  colors_aff = c("yellow2", "red"),
  colors_unaff = c("white", "steelblue4"),
  colors_avail = c("green", "black"),
  colors_na = "grey"
)

# S4 method for class 'Pedigree'
generate_colors(
  obj,
  col_aff = "affected",
  add_to_scale = TRUE,
  col_avail = "avail",
  is_num = NULL,
  mods_aff = NULL,
  threshold = 0.5,
  sup_thres_aff = TRUE,
  keep_full_scale = FALSE,
  breaks = 3,
  colors_aff = c("yellow2", "red"),
  colors_unaff = c("white", "steelblue4"),
  colors_avail = c("green", "black"),
  colors_na = "grey",
  reset = TRUE
)

Arguments

obj

A Pedigree object or a vector containing the affection status for each individuals. The affection status can be numeric or a character.

avail

A logical vector with the availability status of the individuals (i.e. FALSE = not available, TRUE = available, NA = unknown).

mods_aff

Vector of modality to consider as affected in the case where the values is a factor.

is_num

Boolean defining if the values need to be considered as numeric.

keep_full_scale

Boolean defining if the affection values need to be set as a scale. If values is numeric the filling scale will be calculated based on the values and the number of breaks given. If values isn't numeric then each levels will get it's own color

colors_aff

Set of increasing colors to use for the filling of the affected individuls.

colors_unaff

Set of increasing colors to use for the filling of the unaffected individuls.

colors_avail

Set of 2 colors to use for the box's border of an individual. The first color will be used for available individual (avail == 1) and the second for the unavailable individual (avail == 0).

colors_na

Color to use for individuals with no informations.

threshold

Numeric value separating the affected and healthy subject in the case where the values is numeric.

sup_thres_aff

Boolean defining if the affected individual are above the threshold or not. If TRUE, the individuals will be considered affected if the value of values is stricly above the threshold. If FALSE, the individuals will be considered affected if the value is stricly under the threshold.

breaks

Number of breaks to use when using full scale with numeric values. The same number of breaks will be done for values from affected individuals and unaffected individuals.

col_aff

A character vector with the name of the column to be used for the affection status.

add_to_scale

Boolean defining if the scales need to be added to the existing scales or if they need to replace the existing scales.

col_avail

A character vector with the name of the column to be used for the availability status.

reset

If TRUE the scale of the specified column will be reset if already present.

Value

When used with a vector

A list of two elements

  • The list containing the filling colors processed and their description

  • The list containing the border colors processed and their description

When used with a Pedigree object

The Pedigree object with the affected and avail columns processed accordingly as well as the scales slot updated.

Details

The colors will be set using the generate_fill()] and the generate_border() functions respectively for the filling and the border.

Examples


generate_colors(
    c("A", "B", "A", "B", NA, "A", "B", "A", "B", NA),
    c(1, 0, 1, 0, NA, 1, 0, 1, 0, NA),
    mods_aff = "A"
)
#> $fill
#> $fill$mods
#>  [1]  1  0  1  0 NA  1  0  1  0 NA
#> 
#> $fill$affected
#>  [1]  TRUE FALSE  TRUE FALSE    NA  TRUE FALSE  TRUE FALSE    NA
#> 
#> $fill$sc_fill
#>   mods         labels affected  fill density angle
#> 1    1 Affected are A     TRUE   red      NA    NA
#> 2    0  Healthy are B    FALSE white      NA    NA
#> 5   NA           <NA>       NA  grey      NA    NA
#> 
#> 
#> $bord
#> $bord$mods
#>  [1]  1  0  1  0 NA  1  0  1  0 NA
#> 
#> $bord$avail
#>  [1]  TRUE FALSE  TRUE FALSE    NA  TRUE FALSE  TRUE FALSE    NA
#> 
#> $bord$sc_bord
#>   column mods border        labels
#> 1  avail   NA   grey            NA
#> 2  avail    1  green     Available
#> 3  avail    0  black Non Available
#> 
#> 

generate_colors(
    c(10, 0, 5, 7, NA, 6, 2, 1, 3, NA),
    c(1, 0, 1, 0, NA, 1, 0, 1, 0, NA),
    threshold = 3, keep_full_scale = TRUE
)
#> $fill
#> $fill$mods
#>  [1]  6  1  4  5 NA  4  2  1  3 NA
#> 
#> $fill$affected
#>  [1]  TRUE FALSE  TRUE  TRUE    NA  TRUE FALSE FALSE FALSE    NA
#> 
#> $fill$sc_fill
#>   mods                        labels affected    fill density angle
#> 1    6   Affected > to 3 : (8.33,10]     TRUE #FF0000      NA    NA
#> 2    1  Healthy <= to 3 : [-0.003,1]    FALSE #FFFFFF      NA    NA
#> 3    4    Affected > to 3 : [5,6.67]     TRUE #EEEE00      NA    NA
#> 4    5 Affected > to 3 : (6.67,8.33]     TRUE #F67700      NA    NA
#> 5   NA                       NA : NA       NA    grey      NA    NA
#> 7    2       Healthy <= to 3 : (1,2]    FALSE #9AB1C4      NA    NA
#> 9    3       Healthy <= to 3 : (2,3]    FALSE #36648B      NA    NA
#> 
#> 
#> $bord
#> $bord$mods
#>  [1]  1  0  1  0 NA  1  0  1  0 NA
#> 
#> $bord$avail
#>  [1]  TRUE FALSE  TRUE FALSE    NA  TRUE FALSE  TRUE FALSE    NA
#> 
#> $bord$sc_bord
#>   column mods border        labels
#> 1  avail   NA   grey            NA
#> 2  avail    1  green     Available
#> 3  avail    0  black Non Available
#> 
#> 
data("sampleped")
ped <- Pedigree(sampleped)
ped <- generate_colors(ped, "affected", add_to_scale=FALSE)
scales(ped)
#> An object of class "Scales"
#> Slot "fill":
#>   order column_values   column_mods mods                   labels affected
#> 1     1      affected affected_mods    0 Healthy are FALSE / TRUE    FALSE
#> 2     1      affected affected_mods   NA                     <NA>       NA
#>    fill density angle
#> 1 white      NA    NA
#> 2  grey      NA    NA
#> 
#> Slot "border":
#>   column_values column_mods mods        labels border
#> 1         avail  avail_mods   NA            NA   grey
#> 2         avail  avail_mods    1     Available  green
#> 3         avail  avail_mods    0 Non Available  black
#>