autoplot: Generate a 'ggplot' for Bland-Altman Plot and Regression Plot

In mcradds: Processing and Analyzing of Diagnostics Trials

Generate a ggplot for Bland-Altman Plot and Regression Plot

Description

Draw a ggplot-based difference Bland-Altman plot of reference assay vs. test assay for BAsummary object, and a regression plot for MCResult. Also Providing the necessary and useful option arguments for presentation.

Usage

autoplot(object, ...)

## S4 method for signature 'BAsummary'
autoplot(
  object,
  type = c("absolute", "relative"),
  color = "black",
  fill = "lightgray",
  size = 1.5,
  shape = 21,
  jitter = FALSE,
  ref.line = TRUE,
  ref.line.params = list(col = "blue", linetype = "solid", size = 1),
  ci.line = FALSE,
  ci.line.params = list(col = "blue", linetype = "dashed"),
  loa.line = TRUE,
  loa.line.params = list(col = "blue", linetype = "dashed"),
  label = TRUE,
  label.digits = 4,
  label.params = list(col = "black", size = 4),
  x.nbreak = NULL,
  y.nbreak = NULL,
  x.title = NULL,
  y.title = NULL,
  main.title = NULL
)

## S4 method for signature 'MCResult'
autoplot(
  object,
  color = "black",
  fill = "lightgray",
  size = 1.5,
  shape = 21,
  jitter = FALSE,
  identity = TRUE,
  identity.params = list(col = "gray", linetype = "dashed"),
  reg = TRUE,
  reg.params = list(col = "blue", linetype = "solid"),
  equal.axis = FALSE,
  legend.title = TRUE,
  legend.digits = 2,
  x.nbreak = NULL,
  y.nbreak = NULL,
  x.title = NULL,
  y.title = NULL,
  main.title = NULL
)

Arguments

object	(BAsummary, MCResult) input, depending on which function you have done, blandAltman() or mcreg().
...	not used.
type	(string) difference type from input, default is 'absolute'.
color, fill	(string) point colors.
size	(numeric) the size of points.
shape	(integer) the ggplot shape of points.
jitter	(logical) whether to add a small amount of random variation to the location of points.
ref.line	(logical) whether to plot a 'mean' line, default is TRUE.
ref.line.params, ci.line.params, loa.line.params	(list) parameters (color, linetype, linewidth) for the argument 'ref.line', 'ci.line' and 'loa.line'; eg. ref.line.params = list(col = "blue", linetype = "solid", linewidth = 1).
ci.line	(logical) whether to plot a confidence interval line of 'mean', default is FALSE.
loa.line	(logical) whether to plot limit of agreement line, default is TRUE.
label	(logical) whether to add specific value label for each line (ref.line, ci.line and loa.line). Only be shown when the line is defined as TRUE.
label.digits	(integer) the number of digits after the decimal point in the each label.
label.params	(list) parameters (color, size, fontface) for the argument 'label'.
x.nbreak, y.nbreak	(integer) an integer guiding the number of major breaks of x-axis and y-axis.
x.title, y.title, main.title	(string) the x-axis, y-axis and main title of plot.
identity	(logical) whether to add identity line, default is TRUE.
identity.params, reg.params	(list) parameters (color, linetype) for the argument 'identity' and 'reg'; eg. identity.params = list(col = "gray", linetype = "dashed").
reg	(logical) whether to add regression line where the slope and intercept are obtained from mcr::mcreg() function, default is TRUE.
equal.axis	(logical) whether to adjust the ranges of x-axis and y-axis are identical. If equal.axis = TRUE, x-axis will be equal to y-axis.
legend.title	(logical) whether to present the title in the legend.
legend.digits	(integer) the number of digits after the decimal point in the legend.

Value

A ggplot based Bland-Altman plot or regression plot that can be easily customized using additional ggplot functions.

Note

If you'd like to alter any part that this autoplot function haven't provided, adding other ggplot statements are suggested.

See Also

h_difference() to see the type details.

mcr::mcreg() to see the regression parameters.

Examples

# Specify the type for difference plot
data("platelet")
object <- blandAltman(x = platelet$Comparative, y = platelet$Candidate)
autoplot(object)
autoplot(object, type = "relative")

# Set the addition parameters for `geom_point`
autoplot(object,
  type = "relative",
  jitter = TRUE,
  fill = "lightblue",
  color = "grey",
  size = 2
)

# Set the color and line type for reference and limits of agreement lines
autoplot(object,
  type = "relative",
  ref.line.params = list(col = "red", linetype = "solid"),
  loa.line.params = list(col = "grey", linetype = "solid")
)

# Set label color, size and digits
autoplot(object,
  type = "absolute",
  ref.line.params = list(col = "grey"),
  loa.line.params = list(col = "grey"),
  label.digits = 2,
  label.params = list(col = "grey", size = 3, fontface = "italic")
)

# Add main title, X and Y axis titles, and adjust X ticks.
autoplot(object,
  type = "absolute",
  x.nbreak = 6,
  main.title = "Bland-Altman Plot",
  x.title = "Mean of Test and Reference Methods",
  y.title = "Reference - Test"
)
# Using the default arguments for regression plot
data("platelet")
fit <- mcreg(
  x = platelet$Comparative, y = platelet$Candidate,
  method.reg = "Deming", method.ci = "jackknife"
)
autoplot(fit)

# Only present the regression line and alter the color and shape.
autoplot(fit,
  identity = FALSE,
  reg.params = list(col = "grey", linetype = "dashed"),
  legend.title = FALSE,
  legend.digits = 4
)

mcradds documentation built on Sept. 11, 2024, 5:33 p.m.