blandr.plot.ggplot: Bland-Altman plotting function, using ggplot2

In adamleejohnson/R-ajtools: AJ's R Tools

Bland-Altman plotting function, using ggplot2

Description

Draws a Bland-Altman plot using data calculated using the other functions, using ggplot2

Usage

blandr.plot.ggplot(
  statistics.results,
  method1name = "Method 1",
  method2name = "Method 2",
  plotTitle = "Bland-Altman plot for comparison of 2 methods",
  point_size = 0.8,
  ciDisplay = TRUE,
  ciShading = TRUE,
  ciFillColors = c("steelblue3", "gray85"),
  normalLow = FALSE,
  normalHigh = FALSE,
  overlapping = FALSE,
  x.plot.mode = "means",
  y.plot.mode = "difference",
  plotProportionalBias = FALSE,
  plotProportionalBias.se = TRUE,
  assume.differences.are.normal = TRUE
)

Arguments

statistics.results	A list of statistics generated by the blandr.statistics function: see the function's return list to see what variables are passed to this function
method1name	(Optional) Plotting name for 1st method, default "Method 1"
method2name	(Optional) Plotting name for 2nd method, default "Method 2"
plotTitle	(Optional) Title name, default "Bland-Altman plot for comparison of 2 methods"
point_size	(Optional) Default = 0.8
ciDisplay	(Optional) TRUE/FALSE switch to plot confidence intervals for bias and limits of agreement, default is TRUE
ciShading	(Optional) TRUE/FALSE switch to plot confidence interval shading to plot, default is TRUE
ciFillColors	(Optional) 2-vector of colors to use in the bias shading and confidence band shading
normalLow	(Optional) If there is a normal range, entering a continuous variable will plot a vertical line on the plot to indicate its lower boundary
normalHigh	(Optional) If there is a normal range, entering a continuous variable will plot a vertical line on the plot to indicate its higher boundary
overlapping	(Optional) TRUE/FALSE switch to increase size of plotted point if multiple values using ggplot's geom_count, deafault=FALSE. Not currently recommend until I can tweak the graphics to make them better
x.plot.mode	(Optional) Switch to change x-axis from being plotted by means (="means") or by either 1st method (="method1") or 2nd method (="method2"). Default is "means". Anything other than "means" will switch to default mode.
y.plot.mode	(Optional) Switch to change y-axis from being plotted by difference (="difference") or by proportion magnitude of measurements (="proportion"). Default is "difference". Anything other than "proportional" will switch to default mode.
plotProportionalBias	(Optional) TRUE/FALSE switch. Plots a proportional bias line. Default is FALSE.
plotProportionalBias.se	(Optional) TRUE/FALSE switch. If proportional bias line is drawn, switch to plot standard errors. See stat_smooth for details. Default is TRUE.
assume.differences.are.normal	(Optional, not operationally used currently) Assume the difference of means has a normal distribution. Will be used to build further analyses

Value

ba.plot Returns a ggplot data set that can then be plotted

Author(s)

Deepankar Datta [e-mail]

Examples

# Generates two random measurements
measurement1 <- rnorm(100)
measurement2 <- rnorm(100)

# Generates a ggplot
# Do note the ggplot function wasn't meant to be used on it's own
# and is generally called via the bland.altman.display.and.draw function

# Passes data to the blandr.statistics function to generate Bland-Altman statistics
statistics.results <- blandr.statistics(measurement1, measurement2)

# Generates a ggplot, with no optional arguments
blandr.plot.ggplot(statistics.results)

# Generates a ggplot, with title changed
blandr.plot.ggplot(statistics.results, plotTitle = "Bland-Altman example plot")

# Generates a ggplot, with title changed, and confidence intervals off
blandr.plot.ggplot(statistics.results,
  plotTitle = "Bland-Altman example plot",
  ciDisplay = FALSE, ciShading = FALSE
)

adamleejohnson/R-ajtools documentation built on April 4, 2022, 7:24 a.m.