#绘制Bland-Altman 图代码
install.packages("blandr")
library(blandr)
library(ggplot2)
blandr.draw(method1, method2, method1name = "Method 1",
method2name = "Method 2",
plotTitle = "Bland-Altman plot for comparison of 2 methods",
sig.level = 0.95, LoA.mode = 1, annotate = FALSE, ciDisplay = TRUE,
ciShading = TRUE, normalLow = FALSE, normalHigh = FALSE,
lowest_y_axis = FALSE, highest_y_axis = FALSE, point_size = 0.8,
overlapping = FALSE, plotter = "ggplot", x.plot.mode = "means",
y.plot.mode = "difference", plotProportionalBias = FALSE,
plotProportionalBias.se = TRUE, assume.differences.are.normal = TRUE)
Arguments
method1
A list of numbers.
method2
A list of numbers.
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'
sig.level
(Optional) Two-tailed significance level. Expressed from 0 to 1. Defaults to 0.95.
LoA.mode
(Optional) Switch to change how accurately the limits of agreement (LoA) are calculated from the bias and its standard deviation. The default is LoA.mode=1 which calculates LoA with the more accurate 1.96x multiplier. LoA.mode=2 uses the 2x multiplier which was used in the original papers. This should really be kept at default, except to double check calculations in older papers.
annotate
(Optional) TRUE/FALSE switch to provides annotations to plot, default=FALSE
ciDisplay
(Optional) TRUE/FALSE switch to plot confidence intervals for bias and limits of agreement, default=TRUE
ciShading
(Optional) TRUE/FALSE switch to plot confidence interval shading to plot, default=TRUE
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
lowest_y_axis
(Optional) Defaults to NULL If given a continuous variable will use this as the lower boundary of the y axis. Useful if need multiple plots with equivalent y-axes.
highest_y_axis
(Optional) Defaults to NULL If given a continuous variable will use this as the upper boundary of the y axis. Useful if need multiple plots with equivalent y-axes.
point_size
(Optional) Size of marker for each dot. Default is cex=0.8
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
plotter
(Optional- default='ggplot') Selects which graphics engine to use to plot the Bland-Altman charts. 2 options are 'ggplot' or 'rplot'. If unknown parameter sent, will default to 'ggplot'
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
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