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#' @title Bland-Altman drawing function for R
#'
#' @description Bland-Altman drawing function. Depends on the blandr.statistics function in the package. Will generate a plot via the standard R plotting functions.
#'
#' @author Deepankar Datta <deepankar.datta@gmail.com>
#'
#' @note Started 2015-11-14
#' @note Last update 2015-11-19
#' @note Originally designed for LAVAS and CVLA
#'
#' @param 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'
#'
#' @param method1 A vector of numbers corresponding to the results from method 1.
#' @param method2 A vector of numbers corresponding to the results from method 2.
#'
#' @inheritParams blandr.statistics
#' @inheritParams blandr.plot.limits
#' @inheritParams blandr.plot.rplot
#' @inheritParams blandr.plot.ggplot
#'
#' @include blandr.statistics.r
#' @include blandr.plot.limits.r
#' @include blandr.plot.rplot.r
#' @include blandr.plot.ggplot.r
#'
#' @examples
#' # Generates two random measurements
#' measurement1 <- rnorm(100)
#' measurement2 <- rnorm(100)
#'
#' # Generates a plot, with no optional arguments
#' blandr.draw( measurement1 , measurement2 )
#'
#' # Generates a plot, using the in-built R graphics
#' blandr.draw( measurement1 , measurement2 , plotter = 'rplot' )
#'
#' # Generates a plot, with title changed
#' blandr.draw( measurement1 , measurement2 , plotTitle = 'Bland-Altman example plot' )
#'
#' # Generates a plot, with title changed, and confidence intervals off
#' blandr.draw( measurement1 , measurement2 , plotTitle = 'Bland-Altman example plot' ,
#' ciDisplay = FALSE , ciShading = FALSE )
#'
#' @export
blandr.draw <- function( 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
) {
# Passes data to the blandr.statistics function to generate Bland-Altman statistics
statistics.results <- blandr.statistics(method1, method2, sig.level, LoA.mode)
# Passed data to the blandr.plot.limits function to generate plot limits
# Only used for the basic R plots
plot.limits <- blandr.plot.limits(statistics.results, lowest_y_axis, highest_y_axis)
# Plots data, dependent on what has been selected as the 'plotter' option Implemented as
# an if/else statement
if (plotter == "rplot") {
# Pass data to the blandr.basic.plot function to use R's in-built graphics system
blandr.plot.rplot(statistics.results, plot.limits, method1name, method2name, plotTitle,
annotate, ciDisplay, ciShading, normalLow, normalHigh, point_size)
} else {
# Pass data to the blandr.plot.ggplot function to use ggplot2 graphics system
ba.plot <- blandr.plot.ggplot( statistics.results = statistics.results ,
method1name = method1name ,
method2name = method2name ,
plotTitle = plotTitle ,
ciDisplay = ciDisplay ,
ciShading = ciShading ,
normalLow = normalLow ,
normalHigh = normalHigh ,
overlapping = overlapping ,
x.plot.mode = x.plot.mode ,
y.plot.mode = y.plot.mode ,
plotProportionalBias = plotProportionalBias ,
plotProportionalBias.se = plotProportionalBias.se ,
assume.differences.are.normal = assume.differences.are.normal
)
ba.plot
}
# If ggplot has been selected as the drawing function, returns the ggplot data if further
# annotation needs to be done In reality what this checks for if the plotter function IS
# NOT rplot
if (plotter != "rplot") {
return(ba.plot)
}
# END OF FUNCTION
}
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