plot.ba_analysis: Plot method for ba_analysis objects

In valytics: Statistical Methods for Analytical Method Comparison and Validation

Plot method for ba_analysis objects

Description

Creates a Bland-Altman plot (difference vs. average) for visualizing agreement between two measurement methods. The plot displays the bias (mean difference) and limits of agreement with optional confidence intervals.

Usage

## S3 method for class 'ba_analysis'
plot(
  x,
  show_ci = TRUE,
  show_points = TRUE,
  point_alpha = 0.6,
  point_size = 2,
  line_colors = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

## S3 method for class 'ba_analysis'
autoplot(
  object,
  show_ci = TRUE,
  show_points = TRUE,
  point_alpha = 0.6,
  point_size = 2,
  line_colors = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

x	An object of class ba_analysis.
show_ci	Logical; if TRUE (default), displays confidence interval bands for bias and limits of agreement.
show_points	Logical; if TRUE (default), displays individual data points.
point_alpha	Numeric; transparency of points (0-1, default: 0.6).
point_size	Numeric; size of points (default: 2).
line_colors	Named character vector with colors for "bias", "loa", and "ci". Defaults to a clean color scheme.
title	Character; plot title. If NULL (default), generates an automatic title.
xlab	Character; x-axis label. If NULL, uses "Mean of methods".
ylab	Character; y-axis label. If NULL, auto-generates based on difference type.
...	Additional arguments (currently ignored).
object	An object of class ba_analysis.

Details

The Bland-Altman plot displays:

• Points: Each point represents a paired observation, plotted as the difference (y - x) against the average ((x + y) / 2).

• Bias line: Solid horizontal line at the mean difference.

• Limits of agreement: Dashed horizontal lines at bias +/- 1.96 x SD.

• Confidence intervals: Shaded bands showing the uncertainty in the bias and LoA estimates.

Patterns to look for:

• Funnel shape: Suggests proportional bias (variance increases with magnitude).

• Trend: Suggests systematic relationship between difference and magnitude.

• Outliers: Points outside the LoA may warrant investigation.

Value

A ggplot object that can be further customized.

See Also

ba_analysis() for performing the analysis, summary.ba_analysis() for detailed results

Examples

# Basic Bland-Altman plot
set.seed(42)
method_a <- rnorm(50, mean = 100, sd = 15)
method_b <- method_a + rnorm(50, mean = 2, sd = 5)

ba <- ba_analysis(method_a, method_b)
plot(ba)

# Without confidence intervals
plot(ba, show_ci = FALSE)

# Customized appearance
plot(ba,
     point_alpha = 0.8,
     point_size = 3,
     title = "Method Comparison: A vs B")

# Further customization with ggplot2
library(ggplot2)
plot(ba) +
  theme_minimal() +
  scale_color_brewer(palette = "Set1")

# Using autoplot (ggplot2-style)
autoplot(ba)

valytics documentation built on Feb. 19, 2026, 5:06 p.m.