Set Up a Significance Plot Configuration — setup_SignificanceConfig • rtemis.draw

Build a validated configuration with provenance for authored settings.

Usage

setup_SignificanceConfig(
  view = "volcano",
  estimate = "estimate",
  p_value = "p_value",
  label = NULL,
  p_adjust_method = "holm",
  n_tests = NULL,
  p_transform = "neg_log10",
  p_thresh = 0.05,
  x_thresh = 0,
  zero_cap = NULL,
  annotate_n = 7L,
  reference = TRUE,
  legend = TRUE,
  negative_color = "#BE2E5F",
  neutral_color = "#808080",
  positive_color = "#0F6A66",
  alpha = 0.8,
  point_size = 8,
  xlab = NULL,
  ylab = NULL,
  xlim = NULL,
  ylim = NULL,
  margin_top = NULL,
  margin_right = NULL,
  margin_bottom = NULL,
  margin_left = NULL,
  title = NULL,
  dat_path = NULL,
  origin = NULL,
  writer = NULL,
  legend_position = "top",
  legend_placement = "outside",
  group = NULL,
  palette = NULL
)

Arguments

view: Character {"volcano", "manhattan"}: Scatter or categorical bar view.
estimate: Character: Column containing coefficients or other signed effects.
p_value: Character: Column containing unadjusted p-values.
label: Optional Character: Outcome-label column. Unset generates row labels.
p_adjust_method: Character: Method from stats::p.adjust.methods. Adjustment precedes transformation.
n_tests: Optional Integer [1, Inf): Hypothesis-family size, at least the number of supplied rows. Unset counts all rows, including missing p-values.
p_transform: Character {"neg_log10", "identity", "one_minus"}: Named display transform of adjusted p-values.
p_thresh: Numeric (0, 1]: Significance threshold on adjusted p-values; the comparison is strict.
x_thresh: Numeric: Effect threshold separating low and high significant results.
zero_cap: Optional Numeric (0, Inf): Finite display height for zero p-values under neg_log10; must exceed all finite heights and the significance reference. Unset computes a cap one unit above their rounded-up maximum.
annotate_n: Integer [0, Inf): Maximum significant feature labels per side in the volcano view, ranked by raw p-value with input-order ties.
reference: Logical: Show the transformed significance threshold and, for volcanoes, the effect threshold.
legend: Logical: Show the nonempty significance groups.
negative_color: Character: Color for significant effects below x_thresh.
neutral_color: Character: Color for other results, including effects equal to x_thresh.
positive_color: Character: Color for significant effects above x_thresh.
alpha: Numeric [0, 1]: Mark opacity.
point_size: Numeric (0, Inf): Scatter symbol size in pixels.
xlab: Optional Character: X-axis label.
ylab: Optional Character: Y-axis label.
xlim: Optional Numeric: Exactly two increasing finite volcano x-axis limits. Not used by the categorical view.
ylim: Optional Numeric: Exactly two increasing finite y-axis limits.
margin_top: Optional Integer [0, Inf): Top plot margin in pixels.
margin_right: Optional Integer [0, Inf): Right plot margin in pixels.
margin_bottom: Optional Integer [0, Inf): Bottom plot margin in pixels.
margin_left: Optional Integer [0, Inf): Left plot margin in pixels.
title: Optional Character: Chart title. Declared here because it is the one property every chart type has; palette is not (four take a colormap instead), and axis labels and margins are cartesian-only.
dat_path: Optional Character: Path to the data, read at draw time. The serializable alternative to passing data to draw().
origin: Optional Named character: Per-property provenance.
writer: Optional Named character: Interface name and version.
legend_position: Character {"top", "bottom", "left", "right", "top-left", "top-right", "bottom-left", "bottom-right"}: Legend anchor. Top/bottom anchors use horizontal rows; left/right anchors use a vertical column. Corner anchors align within the top or bottom row.
legend_placement: Character {"outside", "inside"}: Relation to the plotting area. Outside placement reserves space for the complete legend; inside placement overlays the data. Neither setting adds a missing legend.
group: Optional Character: Display-group column. Unset colors by significance and effect direction. Missing groups omit marks after full-family adjustment. Groups never change significance thresholds or annotation ranking.
palette: Optional Character vector: Display-group colors in first-appearance order; unset uses the theme. Requires a group binding.

Value

A SignificanceConfig object.

Examples

setup_SignificanceConfig(view = "manhattan", p_adjust_method = "BH")

#> <rtemis.draw::SignificanceConfig>
#>  @ type            : chr "significance"
#>  @ dat_path        : NULL
#>  @ title           : NULL
#>  @ origin          : Named chr [1:32] "default" "default" "default" "default" "user" ...
#>  .. - attr(*, "names")= chr [1:32] "dat_path" "title" "legend_position" "legend_placement" ...
#>  @ writer          : NULL
#>  @ legend_position : chr "top"
#>  @ legend_placement: chr "outside"
#>  @ view            : chr "manhattan"
#>  @ estimate        : chr "estimate"
#>  @ p_value         : chr "p_value"
#>  @ label           : NULL
#>  @ group           : NULL
#>  @ palette         : NULL
#>  @ p_adjust_method : chr "BH"
#>  @ n_tests         : NULL
#>  @ p_transform     : chr "neg_log10"
#>  @ p_thresh        : num 0.05
#>  @ x_thresh        : num 0
#>  @ zero_cap        : NULL
#>  @ annotate_n      : int 7
#>  @ reference       : logi TRUE
#>  @ legend          : logi TRUE
#>  @ negative_color  : chr "#BE2E5F"
#>  @ neutral_color   : chr "#808080"
#>  @ positive_color  : chr "#0F6A66"
#>  @ alpha           : num 0.8
#>  @ point_size      : num 8
#>  @ xlab            : NULL
#>  @ ylab            : NULL
#>  @ xlim            : NULL
#>  @ ylim            : NULL
#>  @ margin_top      : NULL
#>  @ margin_right    : NULL
#>  @ margin_bottom   : NULL
#>  @ margin_left     : NULL