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Create plotly shapes and annotations for statistical test results

Source: R/stat_helper.R
create_stat_annotations.Rd

Converts results from compute_pairwise_stats() into plotly-compatible shapes (brackets) and annotations (text labels). Sorts comparisons so that small-gap brackets are closest to the data and large-gap brackets are higher.

Usage

create_stat_annotations(
  stats_df,
  fig,
  df,
  x,
  y,
  display = "p.adj",
  hide.ns = FALSE,
  sig.threshold = 0.05,
  line.color = "#000000",
  line.width = 1,
  bracket.style = "capped",
  group.by = NULL,
  facet.by = NULL,
  x.order = NULL,
  font.size = 12,
  step.increase = 0.06,
  text.bump = 0.04,
  bracket.inset = 0.025
)

Arguments

stats_df

Data frame from compute_pairwise_stats().

fig

A plotly figure object. Used to detect subplot axis pairs for faceted plots.

df

The original data frame.

x

Character; x-axis column name.

y

Character; y-axis column name.

display

Character; what to display: "p.adj", "p.value", or "symbol". Default "p.adj".

hide.ns

Logical; hide non-significant results. Default FALSE.

sig.threshold

Numeric; significance threshold for determining non-significant results. Default 0.05.

line.color

Character; color for bracket lines. Default "#000000".

line.width

Numeric; width of bracket lines. Default 1.

bracket.style

Character; "capped" for ggpubr-style brackets with vertical ticks, or "flat" for a single horizontal line. Default "capped".

group.by

Character or NULL; nested grouping column.

facet.by

Character or NULL; faceting column.

x.order

Character vector; order of x-axis categories. If NULL, derived from unique values of x column.

font.size

Numeric; size of annotation text. Default 12.

step.increase

Numeric; fraction of y-range for spacing between successive brackets. Default 0.06.

text.bump

Numeric; fraction of y-range for vertical distance of text above the bracket line. Default 0.04.

bracket.inset

Numeric; fixed amount to inset each bracket endpoint from the group center position. Creates visual separation between adjacent brackets at the same y-level. Default 0.025.

Value

A list with components:

annotations

List of plotly annotation objects.

shapes

List of plotly shape objects.

y.max

Numeric; maximum y value needed to accommodate all annotations.

Author

Jared Andrews, Jacob Martin

Examples

stats_df <- compute_pairwise_stats(
    df = example_iris,
    x = "Species",
    y = "Sepal.Length",
    test = "wilcox.test"
)

fig <- plotly::plot_ly(
    data = example_iris, x = ~Species, y = ~Sepal.Length, type = "box"
)

stat_result <- create_stat_annotations(
    stats_df = stats_df,
    fig = fig,
    df = example_iris,
    x = "Species",
    y = "Sepal.Length",
    display = "symbol"
)

names(stat_result)
#> [1] "annotations" "shapes"      "y.max"