Plot signed estimates and raw p-values through SignificanceConfig. The Manhattan view places outcomes in input order; it does not use genomic coordinates. Missing pairs have no marks but remain in the testing family.
Usage
draw_volcano(
x,
pvals,
xnames = NULL,
p_adjust_method = "holm",
p_transform = "neg_log10",
p_thresh = 0.05,
x_thresh = 0,
annotate_n = 7L,
...,
legend_position = "top",
legend_placement = "outside",
theme = NULL,
width = NULL,
height = NULL,
element_id = NULL,
filename = NULL,
group = NULL
)Arguments
- x
Numeric vector: Signed estimates; NA values have no plotted mark.
- pvals
Numeric vector: Raw p-values in
[0, 1], or NA.- xnames
Optional Character vector: One outcome label per estimate.
- p_adjust_method
Character: Method from stats::p.adjust.methods. Adjustment precedes transformation.
- 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.
- annotate_n
Integer [0, Inf): Maximum significant feature labels per side in the volcano view, ranked by raw p-value with input-order ties.
- ...
Additional named settings for
setup_SignificanceConfig(), such asreference,zero_cap,n_tests, colors, axis limits, or margins.- 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.
- theme
Optional Theme: Widget/export theme.
- width, height
Optional Numeric or Character: Widget dimensions.
- element_id
Optional Character: HTML element identifier.
- filename
Optional Character: Static output path, currently SVG.
- group
Optional vector: One display-group label per outcome; unset uses significance and direction. Missing groups omit marks but retain the testing family.
Statistical semantics
P-values are adjusted once over the full supplied family before rows with
missing estimates or p-values are omitted from the marks. Missing hypotheses
still count in n_tests; they do not become observed p-values of one.
Raw and adjusted values remain in the compiled data. Function-valued
transforms are not accepted by this portable configuration.
Under neg_log10, zero p-values have infinite mathematical height. They
retain their zero value but are displayed at zero_cap, identified by
triangles and a caption. No positive p-value is clamped. For identity and
one-minus transforms, zeros are finite and no cap is used.