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Add r-values and significance stars to a correlations heatmap

Source: R/add_r_and_stars.R
add_r_and_stars.Rd

Adds correlation coefficients and significance stars to a heatmap object returned by PlotCorrelationsHeatmap(). This is a downstream annotation helper for SciDataReportR correlation workflows, not a general-purpose plotting function.

Usage

add_r_and_stars(
  res,
  star_from = c("existing", "raw", "fdr", "P", "P_adj", "column"),
  star_col = NULL,
  r_var = "R",
  r_digits = 2,
  r_size = 3,
  r_color = "black",
  r_nudge_y = -0.28,
  star_size = 6,
  star_color = "black",
  star_nudge_y = 0.15,
  remove_existing_stars = TRUE,
  p_breaks = c(-Inf, 0.001, 0.01, 0.05, Inf),
  p_labels = c("***", "**", "*", "")
)

Arguments

res

The list returned by PlotCorrelationsHeatmap(). The object should contain Unadjusted$plot and/or FDRCorrected$plot ggplot objects with plot data columns such as R, P, P_adj, stars, or stars_FDR.

star_from

One of: "existing" (use whatever the chosen plot already mapped as stars), "raw" (use stars or compute from P), "fdr" (use stars_FDR or compute from P_adj), "P","P_adj" (compute from those columns), "column" (use star_col).

star_col

Column name to use when star_from = "column"

r_var

Column name for correlation values (default "R")

r_digits

Decimal places for r labels

r_size, star_size

Text sizes for r and stars

r_color, star_color

Colors for r and stars

r_nudge_y, star_nudge_y

Vertical nudges (r down, stars up)

remove_existing_stars

If TRUE, remove any pre-existing star text layers

p_breaks, p_labels

Cutpoints/labels for computing stars from p

Value

A ggplot with r-values and stars added.

Input requirements

res is expected to be the output of PlotCorrelationsHeatmap(). Use star_from = "raw" for unadjusted p-value stars, star_from = "fdr" for FDR-adjusted stars, or star_from = "existing" to use the star mapping already present in the selected heatmap.

Common downstream use

Add geom_starcaption() to the returned plot to explain the star annotation thresholds in report-ready figures.