In many applied settings, pedigrees include binary phenotypes such as
affected/unaffected status. To incorporate this, use the
status_column argument to point to a column containing the
relevant variable.
data("hazard")
p <- ggPedigree(
hazard,
famID = "famID",
personID = "ID",
status_column = "affected",
config = list(
code_male = 0,
sex_color_include = TRUE,
status_code_affected = TRUE,
status_code_unaffected = FALSE,
status_shape_affected = 4
)
)
p
ggPedigree(
hazard,
famID = "famID",
personID = "ID",
status_column = "affected",
config = list(
code_male = 0,
sex_color_include = FALSE,
status_code_affected = TRUE,
status_code_unaffected = FALSE,
status_label_affected = "Infected",
status_label_unaffected = "Not infected",
status_legend_title = "Status"
)
)
Highlighting Specific Individuals
You can also highlight specific individuals in the pedigree through
other approaches, such as by creating a new column in your data frame.
For example, if you want to highlight Harry Potter and Dudley Dursley,
you can create a new column called proband and set it to
TRUE for those individuals. You can specify the
status_shape_affected to be a star shape (8) and use the
status_column argument to indicate the probands.
df <- potter
df <- df %>%
mutate(proband = ifelse(name %in% c(
"Harry Potter",
"Dudley Dursley"
), TRUE, FALSE))
ggPedigree(
df,
famID = "famID",
personID = "personID",
status_column = "proband",
config = list(
sex_color_include = TRUE,
status_include = TRUE,
status_code_affected = TRUE,
status_code_unaffected = FALSE,
status_shape_affected = 8 # "✨" # star shape
)
)
Highlighting Harry Potter
Alternatively, you can use what I’ve called focal filling. The
focal_fill argument allows you to highlight one person and
their relatives without modifying the data frame. This is particularly
useful when you want to emphasize a specific individual, such as Harry
Potter, in the pedigree plot. The focal_fill_personID
argument allows you to specify the person ID to highlight, and the
focal_fill_include argument determines whether to include
this highlighting in the plot. Other arguments like
focal_fill_method, focal_fill_n_breaks, and
focal_fill_scale_midpoint control the appearance of the
highlighted area. Notably, you can select focal_fill_component to a
specific component, such as “additive”, which will highlight the
additive genetic relatives of the focal person.
ggPedigree(potter,
famID = "famID",
personID = "personID",
config = list(
focal_fill_personID = 7,
focal_fill_include = TRUE,
# focal_fill_high_color = "yellow",
# focal_fill_mid_color = "red",
# focal_fill_low_color = "#0D082AFF",
focal_fill_force_zero = TRUE,
focal_fill_na_value = "black",
focal_fill_scale_midpoint = 0.25,
focal_fill_component = "additive",
focal_fill_method = "gradient",
focal_fill_n_breaks = NULL,
focal_fill_legend_title = "Genetic Relatives \nof Harry Potter",
# "additive",
sex_color_include = FALSE
) # highlight Harry Potter
# config = list(segment_mz_color = NA) # color for monozygotic twins
)
Here we highlight Harry Potter (ID 7) and his relatives in the
pedigree plot. Other components can be highlighted by changing the
focal_fill_component argument. For example, you can set it
to “mitochondrial” to highlight mitochondrial relatives, or “x” to
highlight X-linked relatives. The focal_fill_method can be
set to “gradient” for a smooth gradient effect or “steps” for distinct
color breaks.
m1 <- ggPedigree(potter,
famID = "famID",
personID = "personID",
config = list(
focal_fill_personID = 7,
focal_fill_include = TRUE,
focal_fill_high_color = "green",
# focal_fill_mid_color = "white",
focal_fill_low_color = "black",
focal_fill_scale_midpoint = 0.55,
focal_fill_component = "mitochondrial",
focal_fill_method = "steps",
focal_fill_n_breaks = 19,
focal_fill_legend_show = FALSE,
focal_fill_legend_title = "Mitochondrial Relatives \nof Harry Potter",
sex_color_include = FALSE
) # highlight Harry Potter
# config = list(segment_mz_color = NA) # color for monozygotic twins
) + ggplot2::guides(shape = "none")
m2 <- ggPedigree(potter,
famID = "famID",
personID = "personID",
config = list(
focal_fill_personID = 8,
focal_fill_include = TRUE,
focal_fill_high_color = "orange",
# focal_fill_mid_color = "white",
focal_fill_low_color = "black",
focal_fill_scale_midpoint = 0.55,
focal_fill_component = "mitochondrial",
focal_fill_method = "steps",
focal_fill_n_breaks = 19,
focal_fill_legend_show = FALSE,
focal_fill_legend_title = "Mitochondrial Relatives \nof Ginny Weasley",
sex_color_include = FALSE
) # highlight Harry Potter
# config = list(segment_mz_color = NA) # color for monozygotic twins
) + ggplot2::guides(shape = "none")
library(patchwork) # for combining plots
m1 + m2 + plot_layout(ncol = 2) +
plot_annotation(title = "Mitochondrial Relatives of Harry Potter and Ginny Weasley")
ggPedigree(potter,
famID = "famID",
personID = "personID",
config = list(
focal_fill_personID = 8,
focal_fill_include = TRUE,
# focal_fill_mid_color = "white",
focal_fill_low_color = "black",
focal_fill_scale_midpoint = 0.55,
focal_fill_component = "matID",
focal_fill_method = "viridis_d",
focal_fill_viridis_option = "turbo",
focal_fill_n_breaks = 19,
focal_fill_legend_show = FALSE,
focal_fill_legend_title = "Mitochondrial Relatives",
sex_color_include = FALSE,
overlay_include = FALSE
) # highlight Harry Potter
# config = list(segment_mz_color = NA) # color for monozygotic twins
) + ggplot2::guides(shape = "none")
