Centralized configuration list used by all gg-based plotting functions. Returns a named list of default settings used by all gg-based plotting functions. This configuration can be overridden by supplying a list of key-value pairs to plotting functions such as `ggPedigree()`, `ggRelatednessMatrix()`, and `ggPhenotypeByDegree()`. Each key corresponds to a configurable plot, layout, or aesthetic behavior.
Usage
getDefaultPlotConfig(
function_name = "getDefaultPlotConfig",
personID = "personID",
status_column = NULL,
alpha_default = 1,
apply_default_scales = TRUE,
apply_default_theme = TRUE,
segment_default_color = "black",
color_palette_default = c("#440154FF", "#FDE725FF", "#21908CFF"),
color_palette_low = "#000004FF",
color_palette_mid = "#56106EFF",
color_palette_high = "#FCFDBFFF",
color_scale_midpoint = 0.5,
color_scale_theme = "ggthemes::calc",
alpha = alpha_default,
plot_title = NULL,
plot_subtitle = NULL,
value_rounding_digits = 5,
code_male = 1,
filter_n_pairs = 500,
filter_degree_min = 0,
filter_degree_max = 7,
drop_classic_kin = FALSE,
drop_non_classic_sibs = TRUE,
use_only_classic_kin = TRUE,
use_relative_degree = TRUE,
group_by_kin = TRUE,
match_threshold_percent = 10,
max_degree_levels = 12,
grouping_column = "mtdna_factor",
annotate_include = TRUE,
annotate_x_shift = -0.1,
annotate_y_shift = 0.005,
label_include = TRUE,
label_column = "personID",
label_method = "ggrepel",
label_max_overlaps = 15,
label_nudge_x = 0,
label_nudge_y = -0.1,
label_segment_color = NA,
label_text_angle = 0,
label_text_size = 2,
label_text_color = "black",
point_size = 4,
outline_include = FALSE,
outline_multiplier = 1.25,
outline_color = "black",
tooltip_include = TRUE,
tooltip_columns = c("ID1", "ID2", "value"),
axis_x_label = NULL,
axis_y_label = NULL,
axis_text_angle_x = 90,
axis_text_angle_y = 0,
axis_text_size = 8,
axis_text_color = "black",
generation_height = 1,
generation_width = 1,
ped_packed = TRUE,
ped_align = TRUE,
ped_width = 15,
segment_linewidth = 0.5,
segment_linetype = 1,
segment_lineend = "round",
segment_linejoin = "round",
segment_offspring_color = segment_default_color,
segment_parent_color = segment_default_color,
segment_self_color = segment_default_color,
segment_sibling_color = segment_default_color,
segment_spouse_color = segment_default_color,
segment_mz_color = segment_default_color,
segment_mz_linetype = 1,
segment_mz_alpha = 1,
segment_mz_t = 0.6,
segment_self_linetype = "dotdash",
segment_self_linewidth = 0.25,
segment_self_alpha = 0.5,
segment_self_angle = 90,
segment_self_curvature = -0.2,
sex_color_include = TRUE,
sex_legend_title = "Sex",
sex_shape_labels = c("Female", "Male", "Unknown"),
sex_color_palette = color_palette_default,
sex_shape_female = 16,
sex_shape_male = 15,
sex_shape_unknown = 18,
status_include = TRUE,
status_code_affected = 1,
status_code_unaffected = 0,
status_label_affected = "Affected",
status_label_unaffected = "Unaffected",
status_alpha_affected = 1,
status_alpha_unaffected = 0,
status_color_palette = c(color_palette_default[1], color_palette_default[2]),
status_color_affected = "black",
status_color_unaffected = color_palette_default[2],
status_shape_affected = 4,
status_legend_title = "Affected",
status_legend_show = FALSE,
overlay_shape = 4,
overlay_code_affected = 1,
overlay_code_unaffected = 0,
overlay_label_affected = "Affected",
overlay_label_unaffected = "Unaffected",
overlay_alpha_affected = 1,
overlay_alpha_unaffected = 0,
overlay_color = "black",
overlay_include = FALSE,
overlay_legend_title = "Overlay",
overlay_legend_show = FALSE,
focal_fill_include = FALSE,
focal_fill_legend_show = TRUE,
focal_fill_personID = 1,
focal_fill_legend_title = "Focal Fill",
focal_fill_high_color = "#FDE725FF",
focal_fill_mid_color = "#9F2A63FF",
focal_fill_low_color = "#0D082AFF",
focal_fill_scale_midpoint = color_scale_midpoint,
focal_fill_method = "gradient",
focal_fill_component = "additive",
focal_fill_n_breaks = NULL,
focal_fill_na_value = "black",
focal_fill_shape = 21,
focal_fill_force_zero = FALSE,
focal_fill_hue_range = c(0, 360),
focal_fill_chroma = 50,
focal_fill_lightness = 50,
focal_fill_hue_direction = "horizontal",
focal_fill_viridis_option = "D",
focal_fill_viridis_begin = 0,
focal_fill_viridis_end = 1,
focal_fill_viridis_direction = 1,
ci_include = TRUE,
ci_ribbon_alpha = 0.3,
tile_color_palette = c("white", "gold", "red"),
tile_interpolate = TRUE,
tile_color_border = NA,
tile_cluster = TRUE,
tile_geom = "geom_tile",
matrix_diagonal_include = TRUE,
matrix_upper_triangle_include = FALSE,
matrix_lower_triangle_include = TRUE,
matrix_sparse = FALSE,
matrix_isChild_method = "partialparent",
return_static = TRUE,
return_widget = FALSE,
return_interactive = FALSE,
return_midparent = FALSE,
debug = FALSE,
override_many2many = FALSE,
...
)Arguments
- function_name
The name of the function calling this configuration.
- personID
The column name for person identifiers in the data.
- status_column
The column name for affected status in the data.
- alpha_default
Default alpha transparency level.
- apply_default_scales
Whether to apply default color scales.
- apply_default_theme
Whether to apply default ggplot2 theme.
- segment_default_color
A character string for the default color of segments in the plot.
- color_palette_default
A character vector of default colors for the plot.
- color_palette_low
Color for the low end of a gradient.
- color_palette_mid
Color for the midpoint of a gradient.
- color_palette_high
Color for the high end of a gradient.
- color_scale_midpoint
Midpoint value for continuous color scales.
- color_scale_theme
Name of the color scale used (e.g., "ggthemes::calc").
- alpha
Default alpha transparency for plot elements.
- plot_title
Main title of the plot.
- plot_subtitle
Subtitle of the plot.
- value_rounding_digits
Number of digits to round displayed values.
- code_male
Integer code for males in data.
- filter_n_pairs
Threshold to filter maximum number of pairs.
- filter_degree_min
Minimum degree value used in filtering.
- filter_degree_max
Maximum degree value used in filtering.
- drop_classic_kin
Whether to exclude classic kin categories.
- drop_non_classic_sibs
Whether to exclude non-classic sibs.
- use_only_classic_kin
Whether to restrict analysis to classic kinship.
- use_relative_degree
Whether to use relative degrees instead of absolute.
- group_by_kin
Whether to group output by kinship group.
- match_threshold_percent
Kinbin matching threshold as a percentage.
- max_degree_levels
Maximum number of degree levels to show.
- grouping_column
Name of column used for grouping.
- annotate_include
Whether to include annotations.
- annotate_x_shift
Horizontal shift applied to annotation text.
- annotate_y_shift
Vertical shift applied to annotation text.
- label_include
Whether to display labels on plot points.
- label_column
Column to use for text labels.
- label_method
Method used for labeling (e.g., ggrepel, geom_text).
- label_max_overlaps
Maximum number of overlapping labels.
- label_nudge_x
Horizontal nudge for label text.
- label_nudge_y
Vertical nudge for label text.
- label_segment_color
Segment color for label connectors.
- label_text_angle
Text angle for labels.
- label_text_size
Font size for labels.
- label_text_color
Color of the label text.
- point_size
Size of points drawn in plot.
- outline_include
Whether to include outlines around points.
- outline_multiplier
Multiplier to compute outline size from point size.
- outline_color
Color used for point outlines.
- tooltip_include
Whether tooltips are shown in interactive plots.
- tooltip_columns
Columns to include in tooltips.
- axis_x_label
Label for the X-axis.
- axis_y_label
Label for the Y-axis.
- axis_text_angle_x
Angle of X-axis text.
- axis_text_angle_y
Angle of Y-axis text.
- axis_text_size
Font size of axis text.
- axis_text_color
Color of axis text.
- generation_height
Vertical spacing of generations.
- generation_width
Horizontal spacing of generations.
- ped_packed
Whether the pedigree should use packed layout.
- ped_align
Whether to align pedigree generations.
- ped_width
Plot width of the pedigree block.
- segment_linewidth
Line width for segments.
- segment_linetype
Line type for segments.
- segment_lineend
Line end type for segments.
- segment_linejoin
Line join type for segments.
- segment_offspring_color
Color for offspring segments.
- segment_parent_color
Color for parent segments.
- segment_self_color
Color for self-loop segments.
- segment_sibling_color
Color for sibling segments.
- segment_spouse_color
Color for spouse segments.
- segment_mz_color
Color for monozygotic twin segments.
- segment_mz_linetype
Line type for MZ segments.
- segment_mz_alpha
Alpha for MZ segments.
- segment_mz_t
Tuning parameter for MZ segment layout.
- segment_self_linetype
Line type for self-loop segments.
- segment_self_linewidth
Width of self-loop segment lines.
- segment_self_alpha
Alpha value for self-loop segments.
- segment_self_angle
Angle of self-loop segment.
- segment_self_curvature
Curvature of self-loop segment.
- sex_color_include
Whether to color nodes by sex.
- sex_legend_title
Title of the sex legend.
- sex_shape_labels
Labels used in sex legend.
- sex_color_palette
A character vector of colors for sex.
- sex_shape_female
Shape for female nodes.
- sex_shape_male
Shape for male nodes.
- sex_shape_unknown
Shape for unknown sex nodes.
- status_include
Whether to display affected status.
- status_code_affected
Value that encodes affected status.
- status_code_unaffected
Value that encodes unaffected status.
- status_label_affected
Label for affected status.
- status_label_unaffected
Label for unaffected status.
- status_alpha_affected
Alpha for affected individuals.
- status_alpha_unaffected
Alpha for unaffected individuals. Default is 0 (transparent).
- status_color_palette
A character vector of colors for affected status.
- status_color_affected
Color for affected individuals.
- status_color_unaffected
Color for unaffected individuals.
- status_shape_affected
Shape for affected individuals.
- status_legend_title
Title of the status legend.
- status_legend_show
Whether to show the status legend.
- overlay_shape
Shape used for overlaying points in the plot. Default is 4 (cross).
- overlay_code_affected
Code for affected individuals in overlay. Default is 1.
- overlay_code_unaffected
Code for unaffected individuals in overlay. Default is 0.
- overlay_label_affected
Label for affected individuals in overlay. Default is "Affected".
- overlay_label_unaffected
Label for unaffected individuals in overlay. Default is "Unaffected".
- overlay_alpha_affected
Alpha for affected individuals in overlay. Default is 1.
- overlay_alpha_unaffected
Alpha for unaffected individuals in overlay. Default is 0.
- overlay_color
Color for overlay points. Default is "black".
- overlay_include
Whether to include overlay points in the plot. Default is FALSE.
- overlay_legend_title
Title of the overlay legend. Default is "Overlay".
- overlay_legend_show
Whether to show the overlay legend. Default is FALSE.
- focal_fill_include
Whether to fill focal individuals.
- focal_fill_legend_show
Whether to show legend for focal fill.
- focal_fill_personID
ID of focal individual.
- focal_fill_legend_title
Title of focal fill legend.
- focal_fill_high_color
High-end color for focal gradient.
- focal_fill_mid_color
Midpoint color for focal gradient.
- focal_fill_low_color
Low-end color for focal gradient.
- focal_fill_scale_midpoint
Midpoint for focal fill scale.
- focal_fill_method
Method used for focal fill gradient.
- focal_fill_component
Component type for focal fill.
- focal_fill_n_breaks
Number of breaks in focal fill scale.
- focal_fill_na_value
Color for NA values in focal fill.
- focal_fill_shape
Shape used for focal fill points.
- focal_fill_force_zero
Whether to force zero to NA in focal fill.
- focal_fill_hue_range
Hue range for focal fill colors.
- focal_fill_chroma
Chroma value for focal fill colors.
- focal_fill_lightness
Lightness value for focal fill colors.
- focal_fill_hue_direction
Direction of focal fill gradient.
- focal_fill_viridis_option
Option for viridis color scale.
- focal_fill_viridis_begin
Start of viridis color scale.
- focal_fill_viridis_end
End of viridis color scale.
- focal_fill_viridis_direction
Direction of viridis color scale (1 for left to right, -1 for right to left).
- ci_include
Whether to show confidence intervals.
- ci_ribbon_alpha
Alpha level for CI ribbons.
- tile_color_palette
Color palette for matrix plots.
- tile_interpolate
Whether to interpolate colors in matrix tiles.
- tile_color_border
Color border for matrix tiles.
- tile_cluster
Whether to sort by clusters the matrix.
- tile_geom
Geometry type for matrix tiles (e.g., "geom_tile", "geom_raster").
- matrix_diagonal_include
Whether to include diagonal in matrix plots.
- matrix_upper_triangle_include
Whether to include upper triangle in matrix plots.
- matrix_lower_triangle_include
Whether to include lower triangle in matrix plots.
- matrix_sparse
Whether matrix input is sparse.
- matrix_isChild_method
Method used for isChild matrix derivation.
- return_static
Whether to return a static plot.
- return_widget
Whether to return a widget object.
- return_interactive
Whether to return an interactive plot.
- return_midparent
Whether to return midparent values in the plot.
- debug
Whether to enable debugging mode.
- override_many2many
Whether to override many-to-many link logic.
- ...
Additional arguments for future extensibility.