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R/imu.R
In gmwm: Generalized Method of Wavelet Moments
# Copyright (C) 2014 - 2015 James Balamuta, Stephane Guerrier, Roberto Molinari
#
# This file is part of GMWM R Methods Package
#
# The `gmwm` R package is free software: you can redistribute it and/or modify it
# under the terms of the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
# included within the packages source as the LICENSE file.
#
# The `gmwm` R package is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
#
# You should have received a copy of the Attribution-NonCommercial-ShareAlike 4.0 International
# (CC BY-NC-SA 4.0) along with `gmwm`. If not, see <http://www.smac-group.com/licensing/>.
#' @title Create an IMU Object
#' @description Builds an IMU object that provides the program with gyroscope, accelerometer, and axis information per column in the dataset.
#' @param data A \code{vector} which contains data, or a \code{matrix} or \code{data.frame} which contains the data in each column.
#' @param gyros A \code{vector} that contains the index of columns where gyroscope data (such as Gyro. X, Gyro. Y and Gyro. Z) is placed.
#' @param accels A \code{vector} that contains the index of columns where accelerometer data (such as Accel. X, Accel. Y and Accel. Z) is placed.
#' @param axis A \code{vector} that indicates the axises, such as 'X', 'Y', 'Z'.
#' @param freq An \code{integer} that provides the frequency for the data.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @return An \code{imu} object in the following attributes:
#' \describe{
#' \item{sensor}{A \code{vector} that indicates whether data contains gyroscope sensor, accelerometer sensor, or both.}
#' \item{num.sensor}{A \code{vector} that indicates how many columns of data are for gyroscope sensor and accelerometer sensor.}
#' \item{axis}{Axis value such as 'X', 'Y', 'Z'.}
#' \item{freq}{Observations per second.}
#' \item{unit}{String representation of the unit.}
#' \item{name}{Name of the dataset.}
#' }
#' @details
#' \code{data} can be a numeric vector, matrix or data frame.
#'
#' \code{gyros} and \code{accels} cannot be \code{NULL} at the same time, but it will be fine if one of them is \code{NULL}.
#' Also, in order to plot the graph, the length of \code{gyros} and \code{accels} are restricted to be equal.
#'
#' In \code{axis}, duplicate elements are not alowed. If one of parameters between \code{gyros} and \code{accels}
#' is \code{NULL}, specify the axis for each column of data. Check example 1 for help. If both of them are not \code{NULL}, specify the
#' \code{axis} only for one parameter (\code{gyros} or \code{accels}). Check example 3 for help.
#'
#' \code{axis} will be automatically generated if there are less than or equal to 3 axises.
#'
#' @author JJB, Wenchao
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#'
#' # Example 1 - Only gyros
#' test1 = imu(imu6, gyros = 1:3, axis = c('X', 'Y', 'Z'), freq = 100)
#' df1 = wvar.imu(test1)
#' plot(df1)
#'
#' # Example 2 - One gyro and one accelerometer
#' test2 = imu(imu6, gyros = 1, accels = 4, freq = 100)
#' df2 = wvar.imu(test2)
#' plot(df2)
#'
#' # Example 3 - 3 gyros and 3 accelerometers
#' test3 = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#' df3 = wvar.imu(test3)
#' plot(df3)
#'
#' # Example 4 - Custom axis
#' test4 = imu(imu6, gyros = 1:2, accels = 4:5, axis = c('A', 'B'), freq = 100)
#' df4 = wvar.imu(test4)
#' plot(df4)
#' }
imu = function(data, gyros = NULL, accels = NULL, axis = NULL, freq = NULL, unit = NULL, name = NULL){
# 1. Check object
if(is.null(data) || !(is.numeric(data)||is.data.frame(data)||is.matrix(data)) ) {
stop('Data must a numeric vector, data frame, or matrix.')
}
if(is.numeric(data)){
data = as.matrix(data)
}
if(is.data.frame(data)){
data = as.matrix(data)
}
colnames(data) = NULL
# 2. Check gyro and acce
gyro = gyros
acce = accels
ngyros = length(gyro)
nacces = length(acce)
if(is.null(gyro) && is.null(acce)){
stop("At lease one of parameters ('gyros' or 'accels') must be not NULL.")
}else if(!is.null(gyro) && !is.null(acce)){
if(ngyros != nacces){
stop('Data must have equal number of columns for gyroscope and accelerometer sensor.')
}
}
# Merge indices
index = c(gyro, acce)
if(!is.whole(index)){
stop("Paramater 'gyros' and 'accels' must be vectors of integers.")
}
if(any(gyro > ncol(data)) || any(gyro < 1)){
stop('Index for gyroscope is out of bound.')
}
if(any(acce > ncol(data)) || any(acce < 1)){
stop('Index for accelerometer is out of bound.')
}
# 3. Check 'axis': if the user supplies the axis, check input to make sure it is 'good'.
if(!is.null(axis)){
# Duplicate elements are not allowed
if( anyDuplicated(axis) ){
stop('`axis` cannot have duplicated elements.')
}
if(!is.null(gyro) && !is.null(acce)){
if(2*length(axis) != length(index)){
stop('When `gyros` and `accels` are both not NULL, specify the axis only for one sensor.')
}
}else{
if(length(axis) != length(index)){
stop("If only one parameter between 'gyros' and 'accels' are not NULL, specify the axis for each column of data.")
}
}
}else{
# Guess number of sensors
naxis = if(ngyros > 0 && nacces > 0) nacces else nacces + ngyros
# No axis is supplied. try to generate it automatically.
axis = switch(as.character(naxis),
'1' = 'X',
'2' = c('X','Y'),
'3' = c('X','Y','Z'),
stop('axis cannot be automatically generated. Please supply it by specifying "axis = ...".')
)
}
# 4. Check freq
if(is.null(freq)){
freq = 100
warning("`freq` has not been specified. Setting `imu` data's frequency to 100. \n Please recreate the object if the frequency is incorrect.")
}
if(!is(freq,"numeric") || length(freq) != 1){ stop("'freq' must be one numeric number.") }
if(freq <= 0) { stop("'freq' must be larger than 0.") }
# 5. do not need 'start' and 'end'
# 6. unit = NULL
if(!is.null(unit)){
if(!unit %in% c('ns', 'ms', 'sec', 'second', 'min', 'minute', 'hour', 'day', 'mon', 'month', 'year')){
stop('The supported units are "ns", "ms", "sec", "min", "hour", "day", "month", "year". ')
}
}
create_imu(data[,index, drop = F], ngyros, nacces, axis, freq, unit = unit, name = name)
}
#' @title Internal IMU Object Construction
#' @description Internal quick build for imu object.
#' @param data A \code{matrix} with dimensions N x length(index)
#' @param ngyros An \code{integer} containing the number of gyroscopes
#' @param naccess An \code{integer} containing the number of accelerometers
#' @param axis A \code{vector} unique representation of elements e.g. x,y,z or x,y or x.
#' @param freq An \code{integer} that provides the frequency for the data.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @param stype A \code{string} that describes the sensor type. Default value is \code{NULL}.
#' @return An \code{imu} object class.
#' @keywords internal
create_imu = function(data, ngyros, nacces, axis, freq, unit = NULL, name = NULL, stype = NULL){
if(ngyros>0 && nacces>0){
colnames(data) = c(paste(rep('Gyro.', times = ngyros), axis), paste( rep('Accel.', times = nacces), axis))
}else if (ngyros > 0){
colnames(data) = c(paste(rep('Gyro.', times = ngyros), axis))
}else{
colnames(data) = c(paste(rep('Accel.', times = nacces), axis))
}
out = structure(data,
sensor = c(rep("Gyroscope",ngyros > 0), rep("Accelerometer",nacces > 0)),
num.sensor = c(ngyros, nacces),
axis = axis,
freq = freq,
unit = unit,
name = name,
stype = stype,
class = c("imu","matrix"))
}
#' Subset an IMU Object
#'
#' Enables the IMU object to be subsettable. That is, you can load all the data in and then select certain properties.
#' @export
#' @param x A \code{imu} object
#' @param i A \code{integer vector} that specifies the rows to subset. If blank, all rows are selected.
#' @param j A \code{integer vector} that specifies the columns to subset. Special rules apply see details.
#' @param drop A \code{boolean} indicating whether the structure should be preserved or simplified.
#' @return An \code{imu} object class.
#' @details
#' When using the subset operator, note that all the Gyroscopes are placed at the front of object
#' and, then, the Accelerometers are placed.
#'
#' The current implementation of this function requires the following:
#'
#' \itemize{
#' \item There must be the same number of Gyros & Accels per axis option.
#' \itemize{
#' \item Good: 1 \bold{x}-gyro and 1 \bold{x}-accel
#' \item Bad: 1 x-gyro and 1 z-accel
#' }
#' \item The column names are the default cast. (Backend)
#' }
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#'
#' # Create an IMU Object that is full.
#' ex = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#'
#' # Create an IMU object that has only gyros.
#' ex.gyro = ex[,1:3]
#' ex.gyro2 = ex[,c("Gyro. X","Gyro. Y","Gyro. Z")]
#'
#' # Create an IMU object that has only accels.
#' ex.accel = ex[,4:6]
#' ex.accel2 = ex[,c("Accel. X","Accel. Y","Accel. Z")]
#'
#' # Create an IMU object with both gyros and accels on axis X and Y
#' ex.b = ex[,c(1,2,4,5)]
#' ex.b2 = ex[,c("Gyro. X","Gyro. Y","Accel. X","Accel. Y")]
#'
#' }
#'
'[.imu' = function(x, i, j, drop = FALSE){
axis = attr(x,"axis")
sensor = attr(x,"sensor")
num.sensor = attr(x,"num.sensor")
# If j is missing, then it is simply lowering the number of observations!
if(!missing(j)){
# Select column names picked by user
nc = colnames(x)[j]
# Remove structure to get Gyros/Accels
g = gsub("\\..*","",nc)
ng = table(g)
# Remove structure to get at X,Y,Z axis.
g2 = gsub(".* ","",nc)
ng2 = table(g2)
# If we have multiples (e.g. Gyros & Accels), they should have the same amount.
if(length(names(ng)) == 2 && !all(ng == ng[1])){
stop("The same amount of `gyros` and `accels` must be present!")
}
# Check if the axis have the same number.
if(!all(ng2 == ng2[1]) || (length(names(ng)) == 2 && length(names(ng2)) == 2)){
stop("The same amount of `axis` must be present.")
}
axis = names(ng2)
sensor = names(ng)
num.sensor = c({if(!is.na(ng["Gyro"])) ng["Gyro"] else 0}, {if(!is.na(ng["Accel"])) ng["Accel"] else 0})
}
if(drop){
return(NextMethod("[", drop = TRUE))
}
create_imu(NextMethod("[", drop = FALSE),
num.sensor[1], num.sensor[2], axis, attr(x,"freq"), attr(x,"unit"), attr(x,"name"), attr(x,"stype"))
}
#' @title Read an IMU Binary File into R
#'
#' @description
#' Process binary files within the
#'
#' @param file A \code{string} containing file names or paths.
#' @param type A \code{string} that contains a supported IMU type given below.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @details
#' Currently supports the following IMUs:
#' \itemize{
#' \item IMAR
#' \item LN200
#' \item LN200IG
#' \item IXSEA
#' \item NAVCHIP_INT
#' \item NAVCHIP_FLT
#' }
#'
#' We hope to soon be able to support delimited files.
#' @return An \code{imu} object that contains 3 gyroscopes and 3 accelerometers in that order.
#' @references
#' Thanks goes to Philipp Clausen of Labo TOPO, EPFL, Switzerland, topo.epfl.ch, Tel:+41(0)21 693 27 55
#' for providing a matlab function that reads in IMUs.
#' This function is a heavily modified port of MATLAB code into Armadillo/C++.
#' @examples
#' \dontrun{
#' # Relative
#' setwd("F:/")
#'
#' a = read.imu(file = "Documents/James/short_test_data.imu", type = "IXSEA")
#'
#' # Fixed path
#' b = read.imu(file = "F:/Desktop/short_test_data.imu", type = "IXSEA")
#' }
read.imu = function(file, type, unit = NULL, name = NULL){
d = .Call('gmwm_read_imu', PACKAGE = 'gmwm', file_path = file, imu_type = type)
create_imu(d[[1]][,-1], 3, 3, c('X','Y','Z'), d[[2]][1], unit = unit, name = name, stype = type)
}
#' @title Wrapper Function to Plot the Wavelet Variances of IMU Object
#' @description Creates a graph of the wavelet variance for imu object.
#' @method plot wvar.imu
#' @export
#' @param x A \code{wvar.imu} object.
#' @param split A \code{boolean} that indicates whether the graphs should be separate (TRUE) or graphed ontop of each other (FALSE).
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param legend.title A \code{string} that indicates the title of legend. It is onlly used when \code{split = FALSE}.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend. It is onlly used when \code{split = FALSE}.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the graph of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, freq = 100)
#' df = wvar.imu(test)
#'
#' ## Plot in split way
#' plot(df, split = T)
#' plot(df, split = T, CI = F)
#' plot(df, split = T, CI = T, line.color = c('black', 'black'), title.size = 18)
#'
#' ## Plot in combined way
#' plot(df, split = F)
#' plot(df, split = F, line.color = c('black', 'green', 'red'), CI.color = c('black', 'green', 'red'))
#' }
plot.wvar.imu = function(x, split = TRUE, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = NULL, title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13, legend.text.size = 13,
scales = "free_y",...){
autoplot.wvar.imu(x, split = split, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
legend.title = legend.title, legend.key.size = legend.key.size, legend.title.size = legend.title.size, legend.text.size = legend.text.size,
scales = scales)
}
#' @title Plot the Wavelet Variances of IMU Object
#' @description Creates a graph of the wavelet variance for imu object.
#' @method autoplot wvar.imu
#' @export
#' @keywords internal
#' @param object A \code{wvar.imu} object
#' @param split A \code{boolean} that indicates whether the graphs should be separate (TRUE) or graphed ontop of each other (FALSE).
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param legend.title A \code{string} that indicates the title of legend. It is onlly used when \code{split = FALSE}.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend. It is onlly used when \code{split = FALSE}.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the graph of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, freq = 100)
#' df = wvar.imu(test)
#'
#' ## Plot in split way
#' autoplot(df, split = T)
#' autoplot(df, split = T, CI = F)
#' autoplot(df, split = T, CI = T, line.color = c('black', 'black'), title.size = 18)
#'
#' ## Plot in combined way
#' autoplot(df, split = F)
#' autoplot(df, split = F, line.color = c('black', 'green', 'red'),
#' CI.color = c('black', 'green', 'red'))
#' }
autoplot.wvar.imu = function(object, split = TRUE, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = NULL, title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13, legend.text.size = 13,
scales = "free_y",...){
if(!inherits(object, 'wvar.imu')){
stop("This function can only operate on the wvar.imu object. Please use wvar.imu() to create it.")
}
# Handle new wvar.imu data structure
object=object$plotobj
if (split){
if(is.null(CI.color)){
CI.color = "#003C7D"
}
#call the graphical function
autoplot.imu6(object, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
scales = scales)
}else{
#call the graphical function
autoplot.imu2(object, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
legend.title = legend.title, legend.key.size = legend.key.size, legend.title.size = legend.title.size, legend.text.size = legend.text.size,
scales = scales)
}
}
#' @title Plot the Wavelet Variances of IMU Object in Split Type
#' @description Plot each WV variance in a split graph
#' @method autoplot imu6
#' @export
#' @keywords internal
#' @param object A \code{wvar.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the split graphs of an IMU sensor.
autoplot.imu6 = function(object, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
#require packages: scales
#WV=scales=.x=low=high=NULL
value = variable = low = high = .x = NULL
#legend.label = NULL,
#legend.title = '', legend.key.size = 1.3, legend.title.size = 13,
#legend.text.size = 13,
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(2, 2, 2, 2, 1)
default = list(NULL, NULL, NULL, NULL, "#003C7D")
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(1, 1, 1, 1)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
if(CI){
#default setting
#first WV, then CI
if(is.null(line.color)){
line.color = c("#003C7D", "#003C7D")
}
if(is.null(line.type)){
line.type = c('solid', 'dotted')
}
if(is.null(point.size)){
point.size = c(0, 0)
}
if(is.null(point.shape)){
point.shape = c(20, 20)
}
##legend.label
#if(is.null(legend.label)){
# legend.label = c(expression(paste("Empirical WV ", hat(nu))), expression(paste("CI(", hat(nu)," , 0.95)" )) )
#}
# Change the length to meet the requirement of ggplot2
if(length(line.color) == 2){
line.color = c(line.color, line.color[2])
}
if(length(line.type) == 2){
line.type = c(line.type, line.type[2])
}
if(length(point.size) == 2){
point.size = c(point.size, point.size[2])
}
if(length(point.shape) == 2){
point.shape = c(point.shape, point.shape[2])
}
#breaks = c('WV','low')
#legend.fill = c(NA, alpha(CI.color,transparence) )
#legend.linetype = c(line.type[1],'blank' )
#legend.pointshape = c(point.shape[1], NA )
}else{
if(is.null(line.color)){
line.color = c("#003C7D")
}
if(is.null(line.type)){
line.type = c('solid')
}
if(is.null(point.size)){
point.size = c(0)
}
if(is.null(point.shape)){
point.shape = c(20)
}
#if(is.null(legend.label)){
# legend.label = parse(text = c(expression(paste("Empirical WV ", hat(nu))) ) )
#}
#breaks = c('WV')
}
#re-construct the data frame
if(CI){
obj = data.frame(WV = object$WV,
scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}else{
obj = data.frame(WV = object$WV,
scales = object$scales,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
p = ggplot() +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = variable, shape = variable, color = variable)) +
scale_linetype_manual(values = c(line.type)) +
scale_shape_manual(values = c(point.shape))+
scale_size_manual(values = c(point.size)) +
scale_color_manual(values = c(line.color))
#scale_linetype_manual(name = legend.title, values = c(line.type),breaks = breaks, labels = legend.label ) +
#scale_shape_manual(name = legend.title, values = c(point.shape), breaks = breaks, labels = legend.label)+
#scale_size_manual(name = legend.title, values = c(point.size), breaks = breaks, labels = legend.label) +
#scale_color_manual(name = legend.title,values = c(line.color), breaks = breaks, labels = legend.label)
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p +
geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high), fill = alpha(CI.color, transparence), show.legend = F)
# guides(colour = guide_legend(override.aes = list(fill = legend.fill, linetype = legend.linetype, shape = legend.pointshape)))
# CI.color: a hexadecimal color value
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + theme(legend.position='none')+ theme(strip.background = element_rect(fill= facet.label.background) )
p = p + facet_grid(sensor ~ axis, scales = scales) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size= title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
#legend.key.size = unit(legend.key.size, "cm"),
#legend.text = element_text(size = legend.text.size),
#legend.title = element_text(size = legend.title.size),
#legend.background = element_rect(fill="transparent"),
#legend.text.align = 0,
strip.text = element_text(size = facet.label.size) )
p
}
#' @title Plot the Wavelet Variances of IMU Object in Combined Type
#' @description Plot each WV variance in a combined graph
#' @method autoplot imu2
#' @export
#' @keywords internal
#' @param object An \code{wvar.imu} object.
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the graph.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.).
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.).
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param legend.title A \code{string} that indicates the title of legend.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options
#' @return A panel containing the combined graphs of an IMU sensor.
autoplot.imu2 = function(object, CI = T, background = 'white', transparence = 0.1,
line.color = NULL, line.type = NULL,
point.size = NULL, point.shape = NULL, CI.color = NULL,
title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13,
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13,
legend.text.size = 13, facet.label.background = "#003C7D33", scales = "free_y", ...){
value=low=high=WV=.x=axis=NULL
# S1: Checking statement (Reset it to default setting if user passes wrong values)
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
num.axis = length( unique(object$axis) )
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(num.axis, num.axis, num.axis, num.axis, num.axis)
default = list(NULL, NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(num.axis, num.axis, num.axis, num.axis)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
# S2: Auto-select parameters, if not provided by users
if(is.null(line.color)){
line.color = ggColor(num.axis)
}
if(is.null(line.type)){
line.type = rep('solid', num.axis)
}
if(is.null(point.size)){
point.size = rep(0, num.axis)
}
if(is.null(point.shape)){
point.shape = rep(20, num.axis)
}
## Whether give user the right to modify the legend.label: Currently No
if(CI){
if(is.null(CI.color)){
CI.color = ggColor(num.axis) # Change line.color will not automatically change CI.color
}
}
# S2: Rearrange the data into a data frame which can be passed to next step
obj = data.frame(WV = object$WV,
scales = object$scales,
#low = object$low,
#high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
# S3: Generate the graph
p = ggplot() +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = axis, color = axis)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = axis, shape = axis, color = axis) ) +
scale_linetype_manual(name = legend.title, values = c(line.type)) +
scale_shape_manual(name = legend.title, values = c(point.shape))+
scale_size_manual(name = legend.title, values = c(point.size)) +
scale_color_manual(name = legend.title, values = c(line.color))
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p + geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high,
group = axis, fill = axis), alpha = transparence) +
scale_fill_manual(name = legend.title, values = c(CI.color))
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + facet_grid(sensor~., scales = scales) + theme(strip.background = element_rect(fill= facet.label.background) ) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size=title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
legend.key.size = unit(legend.key.size, "cm"),
legend.text = element_text(size = legend.text.size),
legend.title = element_text(size = legend.title.size),
strip.text = element_text(size = facet.label.size) )
p
}
#' @title Wrapper to Automatic Model Selection Results of IMU Object
#' @description Creates a graph of the automatic model selection result containing the empirical and theoretical wavelet variances.
#' @method plot auto.imu
#' @export
#' @param x A \code{auto.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the automatic model selection results of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#' df = auto.imu(test)
#' plot(df)
#' plot(df, CI = F)
#' plot(df, CI = T, line.color = c('black', 'black', 'blue'), title.size = 18)
#' }
plot.auto.imu = function(x, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Automatic Model Selection Results", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
autoplot.auto.imu(x, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
scales = scales)
}
#' @title Automatic Model Selection Results of IMU Object
#' @description Creates a graph of the automatic model selection result containing the empirical and theoretical wavelet variances.
#' @method autoplot auto.imu
#' @export
#' @keywords internal
#' @param object A \code{auto.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the automatic model selection results of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'))
#' df = auto.imu(test)
#' autoplot(df)
#' autoplot(df, CI = F)
#' autoplot(df, CI = T, line.color = c('black', 'black', 'blue'), title.size = 18)
#' }
autoplot.auto.imu = function(object, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Automatic Model Selection Results", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
value = variable = low = high = .x = NULL
###0. param checking
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(3, 3, 3, 3, 1)
default = list(NULL, NULL, NULL, NULL, "#003C7D")
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(2, 2, 2, 2)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
###1. pre-process the object: auto.imu
if(!is(object, "auto.imu") ){
stop('This function can only operate on auto.imu object.')
}
#what is num.sensor and ncols
num.sensor = object[[1]][[2]]$num.sensor
ncols = sum(num.sensor)
#what is freq
freq = object[[1]][[2]]$freq
#what is axis
if(num.sensor[1] == 0 || num.sensor[2] == 0){##only "Accelerometer"/only "Gyroscope"
axis = rep(0, ncols)
for(i in 1:ncols){
axis[i] = object[[i]][[2]]$axis
}
}else{#both
axis = rep(0, ncols/2)
for(i in 1:(ncols/2)){
axis[i] = object[[i]][[2]]$axis
}
}
#assume
obj.list = vector("list", ncols)
for(i in 1:ncols){
obj.list[[i]] = object[[i]][[2]]
######---------------------#######
#obj.list[[i]]$scales = obj.list[[i]]$scales/100
}
##begin: generate the data frame
total.len = 0
each.len = numeric(ncols)
for (i in 1:ncols){
each.len[i] = length(obj.list[[i]]$wv.empir)
total.len = total.len + each.len[i]
}
#Initialize empty data frame with right number of rows
obj = data.frame(scales = numeric(total.len),
emp = numeric(total.len),
low = numeric(total.len),
high = numeric(total.len),
theo = numeric(total.len),
axis = 'AXIS',
sensor = 'SENSOR', stringsAsFactors=FALSE)
if(num.sensor[2] == 0){ ## only "Gyroscope"
#put data into data frame
t = 1
for (i in 1:ncols){
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = axis[i],
sensor = "Gyroscope",
stringsAsFactors=FALSE)
t = t +d
}
}else if(num.sensor[1] == 0){ #only "Accelerometer"
#put data into data frame
t = 1
for (i in 1:ncols){
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = axis[i],
sensor = "Accelerometer",
stringsAsFactors=FALSE)
t = t +d
}
}else{ # both "Gyroscope" and "Accelerometer"
#put data into data frame
t = 1
for (i in 1:ncols){
if(i <= length(axis)){
temp.axis = axis[i]
temp.sensor = "Gyroscope"
}else{
temp.axis = axis[i-length(axis)]
temp.sensor = "Accelerometer"
}
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = temp.axis,
sensor = temp.sensor,
stringsAsFactors=FALSE)
t = t +d
}
}
#-----END OF DATA PROCESSING-------------------------
object = obj
###2. auto-select param
if(CI){
#default setting
#first WV, then CI
if(is.null(line.color)){
line.color = c("#003C7D", "#003C7D", "#F47F24")
}
if(is.null(line.type)){
line.type = c('solid', 'dotted', 'solid')
}
if(is.null(point.size)){
point.size = c(0, 0, 0)
}
if(is.null(point.shape)){
point.shape = c(20, 20, 1)
}
##legend.label
#if(is.null(legend.label)){
# legend.label = c(expression(paste("Empirical WV ", hat(nu))), expression(paste("CI(", hat(nu)," , 0.95)" )) )
#}
#change the length to meet the requirement of ggplot2
if(length(line.color) == 3){
line.color = c(line.color[1:2], line.color[2:3])
}
if(length(line.type) == 3){
line.type = c(line.type[1:2], line.type[2:3])
}
if(length(point.size) == 3){
point.size = c(point.size[1:2], point.size[2:3])
}
if(length(point.shape) == 3){
point.shape = c(point.shape[1:2], point.shape[2:3])
}
#breaks = c('WV','low')
#legend.fill = c(NA, alpha(CI.color,transparence) )
#legend.linetype = c(line.type[1],'blank' )
#legend.pointshape = c(point.shape[1], NA )
}else{
if(is.null(line.color)){
line.color = c("#003C7D", "#F47F24")
}
if(is.null(line.type)){
line.type = c('solid', 'solid')
}
if(is.null(point.size)){
point.size = c(0,0)
}
if(is.null(point.shape)){
point.shape = c(20, 1)
}
#if(is.null(legend.label)){
# legend.label = parse(text = c(expression(paste("Empirical WV ", hat(nu))) ) )
#}
#breaks = c('WV')
}
### 3.reconstruct data frame
#re-construct the data frame
if(CI){
obj = data.frame(scales = object$scales,
emp = object$emp,
low = object$low,
high = object$high,
theo = object$theo,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}else{
obj = data.frame(scales = object$scales,
emp = object$emp,
theo = object$theo,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
### 4. start to plot
p = ggplot() +
#geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable), size = 1) +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = variable, shape = variable, color = variable)) +
scale_linetype_manual(values = c(line.type)) +
scale_shape_manual(values = c(point.shape))+
scale_size_manual(values = c(point.size)) +
scale_color_manual(values = c(line.color))
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p +
geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high), fill = alpha(CI.color, transparence), show.legend = F)
# guides(colour = guide_legend(override.aes = list(fill = legend.fill, linetype = legend.linetype, shape = legend.pointshape)))
#CI.color: a hexadecimal color value
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + theme(legend.position='none') + theme(strip.background = element_rect(fill= facet.label.background) )
p = p + facet_grid(sensor ~ axis, scales = scales) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size= title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
#legend.key.size = unit(legend.key.size, "cm"),
#legend.text = element_text(size = legend.text.size),
#legend.title = element_text(size = legend.title.size),
#legend.background = element_rect(fill="transparent"),
#legend.text.align = 0,
strip.text = element_text(size = facet.label.size) )
p
}
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# Copyright (C) 2014 - 2015 James Balamuta, Stephane Guerrier, Roberto Molinari
#
# This file is part of GMWM R Methods Package
#
# The `gmwm` R package is free software: you can redistribute it and/or modify it
# under the terms of the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
# included within the packages source as the LICENSE file.
#
# The `gmwm` R package is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
#
# You should have received a copy of the Attribution-NonCommercial-ShareAlike 4.0 International
# (CC BY-NC-SA 4.0) along with `gmwm`. If not, see <http://www.smac-group.com/licensing/>.
#' @title Create an IMU Object
#' @description Builds an IMU object that provides the program with gyroscope, accelerometer, and axis information per column in the dataset.
#' @param data A \code{vector} which contains data, or a \code{matrix} or \code{data.frame} which contains the data in each column.
#' @param gyros A \code{vector} that contains the index of columns where gyroscope data (such as Gyro. X, Gyro. Y and Gyro. Z) is placed.
#' @param accels A \code{vector} that contains the index of columns where accelerometer data (such as Accel. X, Accel. Y and Accel. Z) is placed.
#' @param axis A \code{vector} that indicates the axises, such as 'X', 'Y', 'Z'.
#' @param freq An \code{integer} that provides the frequency for the data.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @return An \code{imu} object in the following attributes:
#' \describe{
#' \item{sensor}{A \code{vector} that indicates whether data contains gyroscope sensor, accelerometer sensor, or both.}
#' \item{num.sensor}{A \code{vector} that indicates how many columns of data are for gyroscope sensor and accelerometer sensor.}
#' \item{axis}{Axis value such as 'X', 'Y', 'Z'.}
#' \item{freq}{Observations per second.}
#' \item{unit}{String representation of the unit.}
#' \item{name}{Name of the dataset.}
#' }
#' @details
#' \code{data} can be a numeric vector, matrix or data frame.
#'
#' \code{gyros} and \code{accels} cannot be \code{NULL} at the same time, but it will be fine if one of them is \code{NULL}.
#' Also, in order to plot the graph, the length of \code{gyros} and \code{accels} are restricted to be equal.
#'
#' In \code{axis}, duplicate elements are not alowed. If one of parameters between \code{gyros} and \code{accels}
#' is \code{NULL}, specify the axis for each column of data. Check example 1 for help. If both of them are not \code{NULL}, specify the
#' \code{axis} only for one parameter (\code{gyros} or \code{accels}). Check example 3 for help.
#'
#' \code{axis} will be automatically generated if there are less than or equal to 3 axises.
#'
#' @author JJB, Wenchao
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#'
#' # Example 1 - Only gyros
#' test1 = imu(imu6, gyros = 1:3, axis = c('X', 'Y', 'Z'), freq = 100)
#' df1 = wvar.imu(test1)
#' plot(df1)
#'
#' # Example 2 - One gyro and one accelerometer
#' test2 = imu(imu6, gyros = 1, accels = 4, freq = 100)
#' df2 = wvar.imu(test2)
#' plot(df2)
#'
#' # Example 3 - 3 gyros and 3 accelerometers
#' test3 = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#' df3 = wvar.imu(test3)
#' plot(df3)
#'
#' # Example 4 - Custom axis
#' test4 = imu(imu6, gyros = 1:2, accels = 4:5, axis = c('A', 'B'), freq = 100)
#' df4 = wvar.imu(test4)
#' plot(df4)
#' }
imu = function(data, gyros = NULL, accels = NULL, axis = NULL, freq = NULL, unit = NULL, name = NULL){
# 1. Check object
if(is.null(data) || !(is.numeric(data)||is.data.frame(data)||is.matrix(data)) ) {
stop('Data must a numeric vector, data frame, or matrix.')
}
if(is.numeric(data)){
data = as.matrix(data)
}
if(is.data.frame(data)){
data = as.matrix(data)
}
colnames(data) = NULL
# 2. Check gyro and acce
gyro = gyros
acce = accels
ngyros = length(gyro)
nacces = length(acce)
if(is.null(gyro) && is.null(acce)){
stop("At lease one of parameters ('gyros' or 'accels') must be not NULL.")
}else if(!is.null(gyro) && !is.null(acce)){
if(ngyros != nacces){
stop('Data must have equal number of columns for gyroscope and accelerometer sensor.')
}
}
# Merge indices
index = c(gyro, acce)
if(!is.whole(index)){
stop("Paramater 'gyros' and 'accels' must be vectors of integers.")
}
if(any(gyro > ncol(data)) || any(gyro < 1)){
stop('Index for gyroscope is out of bound.')
}
if(any(acce > ncol(data)) || any(acce < 1)){
stop('Index for accelerometer is out of bound.')
}
# 3. Check 'axis': if the user supplies the axis, check input to make sure it is 'good'.
if(!is.null(axis)){
# Duplicate elements are not allowed
if( anyDuplicated(axis) ){
stop('`axis` cannot have duplicated elements.')
}
if(!is.null(gyro) && !is.null(acce)){
if(2*length(axis) != length(index)){
stop('When `gyros` and `accels` are both not NULL, specify the axis only for one sensor.')
}
}else{
if(length(axis) != length(index)){
stop("If only one parameter between 'gyros' and 'accels' are not NULL, specify the axis for each column of data.")
}
}
}else{
# Guess number of sensors
naxis = if(ngyros > 0 && nacces > 0) nacces else nacces + ngyros
# No axis is supplied. try to generate it automatically.
axis = switch(as.character(naxis),
'1' = 'X',
'2' = c('X','Y'),
'3' = c('X','Y','Z'),
stop('axis cannot be automatically generated. Please supply it by specifying "axis = ...".')
)
}
# 4. Check freq
if(is.null(freq)){
freq = 100
warning("`freq` has not been specified. Setting `imu` data's frequency to 100. \n Please recreate the object if the frequency is incorrect.")
}
if(!is(freq,"numeric") || length(freq) != 1){ stop("'freq' must be one numeric number.") }
if(freq <= 0) { stop("'freq' must be larger than 0.") }
# 5. do not need 'start' and 'end'
# 6. unit = NULL
if(!is.null(unit)){
if(!unit %in% c('ns', 'ms', 'sec', 'second', 'min', 'minute', 'hour', 'day', 'mon', 'month', 'year')){
stop('The supported units are "ns", "ms", "sec", "min", "hour", "day", "month", "year". ')
}
}
create_imu(data[,index, drop = F], ngyros, nacces, axis, freq, unit = unit, name = name)
}
#' @title Internal IMU Object Construction
#' @description Internal quick build for imu object.
#' @param data A \code{matrix} with dimensions N x length(index)
#' @param ngyros An \code{integer} containing the number of gyroscopes
#' @param naccess An \code{integer} containing the number of accelerometers
#' @param axis A \code{vector} unique representation of elements e.g. x,y,z or x,y or x.
#' @param freq An \code{integer} that provides the frequency for the data.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @param stype A \code{string} that describes the sensor type. Default value is \code{NULL}.
#' @return An \code{imu} object class.
#' @keywords internal
create_imu = function(data, ngyros, nacces, axis, freq, unit = NULL, name = NULL, stype = NULL){
if(ngyros>0 && nacces>0){
colnames(data) = c(paste(rep('Gyro.', times = ngyros), axis), paste( rep('Accel.', times = nacces), axis))
}else if (ngyros > 0){
colnames(data) = c(paste(rep('Gyro.', times = ngyros), axis))
}else{
colnames(data) = c(paste(rep('Accel.', times = nacces), axis))
}
out = structure(data,
sensor = c(rep("Gyroscope",ngyros > 0), rep("Accelerometer",nacces > 0)),
num.sensor = c(ngyros, nacces),
axis = axis,
freq = freq,
unit = unit,
name = name,
stype = stype,
class = c("imu","matrix"))
}
#' Subset an IMU Object
#'
#' Enables the IMU object to be subsettable. That is, you can load all the data in and then select certain properties.
#' @export
#' @param x A \code{imu} object
#' @param i A \code{integer vector} that specifies the rows to subset. If blank, all rows are selected.
#' @param j A \code{integer vector} that specifies the columns to subset. Special rules apply see details.
#' @param drop A \code{boolean} indicating whether the structure should be preserved or simplified.
#' @return An \code{imu} object class.
#' @details
#' When using the subset operator, note that all the Gyroscopes are placed at the front of object
#' and, then, the Accelerometers are placed.
#'
#' The current implementation of this function requires the following:
#'
#' \itemize{
#' \item There must be the same number of Gyros & Accels per axis option.
#' \itemize{
#' \item Good: 1 \bold{x}-gyro and 1 \bold{x}-accel
#' \item Bad: 1 x-gyro and 1 z-accel
#' }
#' \item The column names are the default cast. (Backend)
#' }
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#'
#' # Create an IMU Object that is full.
#' ex = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#'
#' # Create an IMU object that has only gyros.
#' ex.gyro = ex[,1:3]
#' ex.gyro2 = ex[,c("Gyro. X","Gyro. Y","Gyro. Z")]
#'
#' # Create an IMU object that has only accels.
#' ex.accel = ex[,4:6]
#' ex.accel2 = ex[,c("Accel. X","Accel. Y","Accel. Z")]
#'
#' # Create an IMU object with both gyros and accels on axis X and Y
#' ex.b = ex[,c(1,2,4,5)]
#' ex.b2 = ex[,c("Gyro. X","Gyro. Y","Accel. X","Accel. Y")]
#'
#' }
#'
'[.imu' = function(x, i, j, drop = FALSE){
axis = attr(x,"axis")
sensor = attr(x,"sensor")
num.sensor = attr(x,"num.sensor")
# If j is missing, then it is simply lowering the number of observations!
if(!missing(j)){
# Select column names picked by user
nc = colnames(x)[j]
# Remove structure to get Gyros/Accels
g = gsub("\\..*","",nc)
ng = table(g)
# Remove structure to get at X,Y,Z axis.
g2 = gsub(".* ","",nc)
ng2 = table(g2)
# If we have multiples (e.g. Gyros & Accels), they should have the same amount.
if(length(names(ng)) == 2 && !all(ng == ng[1])){
stop("The same amount of `gyros` and `accels` must be present!")
}
# Check if the axis have the same number.
if(!all(ng2 == ng2[1]) || (length(names(ng)) == 2 && length(names(ng2)) == 2)){
stop("The same amount of `axis` must be present.")
}
axis = names(ng2)
sensor = names(ng)
num.sensor = c({if(!is.na(ng["Gyro"])) ng["Gyro"] else 0}, {if(!is.na(ng["Accel"])) ng["Accel"] else 0})
}
if(drop){
return(NextMethod("[", drop = TRUE))
}
create_imu(NextMethod("[", drop = FALSE),
num.sensor[1], num.sensor[2], axis, attr(x,"freq"), attr(x,"unit"), attr(x,"name"), attr(x,"stype"))
}
#' @title Read an IMU Binary File into R
#'
#' @description
#' Process binary files within the
#'
#' @param file A \code{string} containing file names or paths.
#' @param type A \code{string} that contains a supported IMU type given below.
#' @param unit A \code{string} that contains the unit expression of the frequency. Default value is \code{NULL}.
#' @param name A \code{string} that provides an identifier to the data. Default value is \code{NULL}.
#' @details
#' Currently supports the following IMUs:
#' \itemize{
#' \item IMAR
#' \item LN200
#' \item LN200IG
#' \item IXSEA
#' \item NAVCHIP_INT
#' \item NAVCHIP_FLT
#' }
#'
#' We hope to soon be able to support delimited files.
#' @return An \code{imu} object that contains 3 gyroscopes and 3 accelerometers in that order.
#' @references
#' Thanks goes to Philipp Clausen of Labo TOPO, EPFL, Switzerland, topo.epfl.ch, Tel:+41(0)21 693 27 55
#' for providing a matlab function that reads in IMUs.
#' This function is a heavily modified port of MATLAB code into Armadillo/C++.
#' @examples
#' \dontrun{
#' # Relative
#' setwd("F:/")
#'
#' a = read.imu(file = "Documents/James/short_test_data.imu", type = "IXSEA")
#'
#' # Fixed path
#' b = read.imu(file = "F:/Desktop/short_test_data.imu", type = "IXSEA")
#' }
read.imu = function(file, type, unit = NULL, name = NULL){
d = .Call('gmwm_read_imu', PACKAGE = 'gmwm', file_path = file, imu_type = type)
create_imu(d[[1]][,-1], 3, 3, c('X','Y','Z'), d[[2]][1], unit = unit, name = name, stype = type)
}
#' @title Wrapper Function to Plot the Wavelet Variances of IMU Object
#' @description Creates a graph of the wavelet variance for imu object.
#' @method plot wvar.imu
#' @export
#' @param x A \code{wvar.imu} object.
#' @param split A \code{boolean} that indicates whether the graphs should be separate (TRUE) or graphed ontop of each other (FALSE).
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param legend.title A \code{string} that indicates the title of legend. It is onlly used when \code{split = FALSE}.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend. It is onlly used when \code{split = FALSE}.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the graph of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, freq = 100)
#' df = wvar.imu(test)
#'
#' ## Plot in split way
#' plot(df, split = T)
#' plot(df, split = T, CI = F)
#' plot(df, split = T, CI = T, line.color = c('black', 'black'), title.size = 18)
#'
#' ## Plot in combined way
#' plot(df, split = F)
#' plot(df, split = F, line.color = c('black', 'green', 'red'), CI.color = c('black', 'green', 'red'))
#' }
plot.wvar.imu = function(x, split = TRUE, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = NULL, title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13, legend.text.size = 13,
scales = "free_y",...){
autoplot.wvar.imu(x, split = split, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
legend.title = legend.title, legend.key.size = legend.key.size, legend.title.size = legend.title.size, legend.text.size = legend.text.size,
scales = scales)
}
#' @title Plot the Wavelet Variances of IMU Object
#' @description Creates a graph of the wavelet variance for imu object.
#' @method autoplot wvar.imu
#' @export
#' @keywords internal
#' @param object A \code{wvar.imu} object
#' @param split A \code{boolean} that indicates whether the graphs should be separate (TRUE) or graphed ontop of each other (FALSE).
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param legend.title A \code{string} that indicates the title of legend. It is onlly used when \code{split = FALSE}.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend. It is onlly used when \code{split = FALSE}.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend. It is onlly used when \code{split = FALSE}.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the graph of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, freq = 100)
#' df = wvar.imu(test)
#'
#' ## Plot in split way
#' autoplot(df, split = T)
#' autoplot(df, split = T, CI = F)
#' autoplot(df, split = T, CI = T, line.color = c('black', 'black'), title.size = 18)
#'
#' ## Plot in combined way
#' autoplot(df, split = F)
#' autoplot(df, split = F, line.color = c('black', 'green', 'red'),
#' CI.color = c('black', 'green', 'red'))
#' }
autoplot.wvar.imu = function(object, split = TRUE, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = NULL, title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13, legend.text.size = 13,
scales = "free_y",...){
if(!inherits(object, 'wvar.imu')){
stop("This function can only operate on the wvar.imu object. Please use wvar.imu() to create it.")
}
# Handle new wvar.imu data structure
object=object$plotobj
if (split){
if(is.null(CI.color)){
CI.color = "#003C7D"
}
#call the graphical function
autoplot.imu6(object, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
scales = scales)
}else{
#call the graphical function
autoplot.imu2(object, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
legend.title = legend.title, legend.key.size = legend.key.size, legend.title.size = legend.title.size, legend.text.size = legend.text.size,
scales = scales)
}
}
#' @title Plot the Wavelet Variances of IMU Object in Split Type
#' @description Plot each WV variance in a split graph
#' @method autoplot imu6
#' @export
#' @keywords internal
#' @param object A \code{wvar.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the split graphs of an IMU sensor.
autoplot.imu6 = function(object, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
#require packages: scales
#WV=scales=.x=low=high=NULL
value = variable = low = high = .x = NULL
#legend.label = NULL,
#legend.title = '', legend.key.size = 1.3, legend.title.size = 13,
#legend.text.size = 13,
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(2, 2, 2, 2, 1)
default = list(NULL, NULL, NULL, NULL, "#003C7D")
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(1, 1, 1, 1)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
if(CI){
#default setting
#first WV, then CI
if(is.null(line.color)){
line.color = c("#003C7D", "#003C7D")
}
if(is.null(line.type)){
line.type = c('solid', 'dotted')
}
if(is.null(point.size)){
point.size = c(0, 0)
}
if(is.null(point.shape)){
point.shape = c(20, 20)
}
##legend.label
#if(is.null(legend.label)){
# legend.label = c(expression(paste("Empirical WV ", hat(nu))), expression(paste("CI(", hat(nu)," , 0.95)" )) )
#}
# Change the length to meet the requirement of ggplot2
if(length(line.color) == 2){
line.color = c(line.color, line.color[2])
}
if(length(line.type) == 2){
line.type = c(line.type, line.type[2])
}
if(length(point.size) == 2){
point.size = c(point.size, point.size[2])
}
if(length(point.shape) == 2){
point.shape = c(point.shape, point.shape[2])
}
#breaks = c('WV','low')
#legend.fill = c(NA, alpha(CI.color,transparence) )
#legend.linetype = c(line.type[1],'blank' )
#legend.pointshape = c(point.shape[1], NA )
}else{
if(is.null(line.color)){
line.color = c("#003C7D")
}
if(is.null(line.type)){
line.type = c('solid')
}
if(is.null(point.size)){
point.size = c(0)
}
if(is.null(point.shape)){
point.shape = c(20)
}
#if(is.null(legend.label)){
# legend.label = parse(text = c(expression(paste("Empirical WV ", hat(nu))) ) )
#}
#breaks = c('WV')
}
#re-construct the data frame
if(CI){
obj = data.frame(WV = object$WV,
scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}else{
obj = data.frame(WV = object$WV,
scales = object$scales,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
p = ggplot() +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = variable, shape = variable, color = variable)) +
scale_linetype_manual(values = c(line.type)) +
scale_shape_manual(values = c(point.shape))+
scale_size_manual(values = c(point.size)) +
scale_color_manual(values = c(line.color))
#scale_linetype_manual(name = legend.title, values = c(line.type),breaks = breaks, labels = legend.label ) +
#scale_shape_manual(name = legend.title, values = c(point.shape), breaks = breaks, labels = legend.label)+
#scale_size_manual(name = legend.title, values = c(point.size), breaks = breaks, labels = legend.label) +
#scale_color_manual(name = legend.title,values = c(line.color), breaks = breaks, labels = legend.label)
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p +
geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high), fill = alpha(CI.color, transparence), show.legend = F)
# guides(colour = guide_legend(override.aes = list(fill = legend.fill, linetype = legend.linetype, shape = legend.pointshape)))
# CI.color: a hexadecimal color value
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + theme(legend.position='none')+ theme(strip.background = element_rect(fill= facet.label.background) )
p = p + facet_grid(sensor ~ axis, scales = scales) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size= title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
#legend.key.size = unit(legend.key.size, "cm"),
#legend.text = element_text(size = legend.text.size),
#legend.title = element_text(size = legend.title.size),
#legend.background = element_rect(fill="transparent"),
#legend.text.align = 0,
strip.text = element_text(size = facet.label.size) )
p
}
#' @title Plot the Wavelet Variances of IMU Object in Combined Type
#' @description Plot each WV variance in a combined graph
#' @method autoplot imu2
#' @export
#' @keywords internal
#' @param object An \code{wvar.imu} object.
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the graph.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.).
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.).
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param legend.title A \code{string} that indicates the title of legend.
#' @param legend.key.size A \code{double} that indicates the size of key (in centermeters) on legend.
#' @param legend.title.size An \code{integer} that indicates the size of title on legend.
#' @param legend.text.size An \code{integer} that indicates the size of key label on legend.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options
#' @return A panel containing the combined graphs of an IMU sensor.
autoplot.imu2 = function(object, CI = T, background = 'white', transparence = 0.1,
line.color = NULL, line.type = NULL,
point.size = NULL, point.shape = NULL, CI.color = NULL,
title = "Haar Wavelet Variance Representation", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13,
legend.title = 'Axis', legend.key.size = 1.3, legend.title.size = 13,
legend.text.size = 13, facet.label.background = "#003C7D33", scales = "free_y", ...){
value=low=high=WV=.x=axis=NULL
# S1: Checking statement (Reset it to default setting if user passes wrong values)
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
num.axis = length( unique(object$axis) )
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(num.axis, num.axis, num.axis, num.axis, num.axis)
default = list(NULL, NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(num.axis, num.axis, num.axis, num.axis)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
# S2: Auto-select parameters, if not provided by users
if(is.null(line.color)){
line.color = ggColor(num.axis)
}
if(is.null(line.type)){
line.type = rep('solid', num.axis)
}
if(is.null(point.size)){
point.size = rep(0, num.axis)
}
if(is.null(point.shape)){
point.shape = rep(20, num.axis)
}
## Whether give user the right to modify the legend.label: Currently No
if(CI){
if(is.null(CI.color)){
CI.color = ggColor(num.axis) # Change line.color will not automatically change CI.color
}
}
# S2: Rearrange the data into a data frame which can be passed to next step
obj = data.frame(WV = object$WV,
scales = object$scales,
#low = object$low,
#high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
# S3: Generate the graph
p = ggplot() +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = axis, color = axis)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = axis, shape = axis, color = axis) ) +
scale_linetype_manual(name = legend.title, values = c(line.type)) +
scale_shape_manual(name = legend.title, values = c(point.shape))+
scale_size_manual(name = legend.title, values = c(point.size)) +
scale_color_manual(name = legend.title, values = c(line.color))
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p + geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high,
group = axis, fill = axis), alpha = transparence) +
scale_fill_manual(name = legend.title, values = c(CI.color))
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + facet_grid(sensor~., scales = scales) + theme(strip.background = element_rect(fill= facet.label.background) ) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size=title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
legend.key.size = unit(legend.key.size, "cm"),
legend.text = element_text(size = legend.text.size),
legend.title = element_text(size = legend.title.size),
strip.text = element_text(size = facet.label.size) )
p
}
#' @title Wrapper to Automatic Model Selection Results of IMU Object
#' @description Creates a graph of the automatic model selection result containing the empirical and theoretical wavelet variances.
#' @method plot auto.imu
#' @export
#' @param x A \code{auto.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the automatic model selection results of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'), freq = 100)
#' df = auto.imu(test)
#' plot(df)
#' plot(df, CI = F)
#' plot(df, CI = T, line.color = c('black', 'black', 'blue'), title.size = 18)
#' }
plot.auto.imu = function(x, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Automatic Model Selection Results", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
autoplot.auto.imu(x, CI = CI, background = background, transparence = transparence, line.color = line.color,
line.type = line.type, point.size = point.size, point.shape = point.shape,
CI.color = CI.color, title = title, title.size= title.size,
axis.label.size = axis.label.size, axis.tick.size = axis.tick.size,
axis.x.label = axis.x.label,
axis.y.label = axis.y.label,
facet.label.size = facet.label.size, facet.label.background = facet.label.background,
scales = scales)
}
#' @title Automatic Model Selection Results of IMU Object
#' @description Creates a graph of the automatic model selection result containing the empirical and theoretical wavelet variances.
#' @method autoplot auto.imu
#' @export
#' @keywords internal
#' @param object A \code{auto.imu} object
#' @param CI A \code{boolean} that indicates whether the confidence interval should be plotted.
#' @param background A \code{string} that determines the graph background. It can be \code{'grey'} or \code{'white'}.
#' @param transparence A \code{double} that ranges from 0 to 1 that controls the transparency of the confidence interval.
#' @param line.color A \code{vector} of \code{string} that indicates the color of the line drawn (e.g. black, blue, red, etc.)
#' @param line.type A \code{vector} of \code{string} that indicates the type of line (e.g. solid, dotted, etc.)
#' @param point.size A \code{vector} of \code{integer} that indicates the size of points on lines.
#' @param point.shape A \code{vector} of \code{integer} that indicates the shape of points on lines.
#' @param CI.color A \code{string} that indicates the color of the confidence interval (e.g. black, red, #003C7D, etc.)
#' @param title A \code{string} that indicates the title of the graph.
#' @param title.size An \code{integer} that indicates the size of title.
#' @param axis.label.size An \code{integer} that indicates the size of label.
#' @param axis.tick.size An \code{integer} that indicates the size of tick mark.
#' @param axis.x.label A \code{string} that indicates the label on x axis.
#' @param axis.y.label A \code{string} that indicates the label on y axis.
#' @param facet.label.size An \code{integer} that indicates the size of facet label.
#' @param facet.label.background A \code{string} that indicates the background color of the facet label.
#' @param scales Same as \code{scales} in \code{facet_grid()} in \code{ggplot2} package: should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x", "free_y"). The default is "free_y" in this function.
#' @param ... Additional options.
#' @return A panel containing the automatic model selection results of an IMU sensor.
#' @examples
#' \dontrun{
#' if(!require("imudata")){
#' install_imudata()
#' library("imudata")
#' }
#'
#' data(imu6)
#' test = imu(imu6, gyros = 1:3, accels = 4:6, axis = c('X', 'Y', 'Z'))
#' df = auto.imu(test)
#' autoplot(df)
#' autoplot(df, CI = F)
#' autoplot(df, CI = T, line.color = c('black', 'black', 'blue'), title.size = 18)
#' }
autoplot.auto.imu = function(object, CI = TRUE, background = 'white', transparence = 0.1, line.color = NULL,
line.type = NULL, point.size = NULL, point.shape = NULL,
CI.color = "#003C7D", title = "Automatic Model Selection Results", title.size= 15,
axis.label.size = 13, axis.tick.size = 11,
axis.x.label = expression(paste("Scale ", tau)),
axis.y.label = expression(paste("Wavelet Variance ", nu)),
facet.label.size = 13, facet.label.background = "#003C7D33",
scales = "free_y",...){
value = variable = low = high = .x = NULL
###0. param checking
if( !(background %in% c('grey','gray', 'white')) ){
warning("Parameter background: No such option. Default setting is used.")
background = 'white'
}
if(CI){
params = c('line.color', 'line.type', 'point.size', 'point.shape', 'CI.color')
requireLength = c(3, 3, 3, 3, 1)
default = list(NULL, NULL, NULL, NULL, "#003C7D")
nullIsFine = c(rep(T,5))
}else{
params = c('line.color', 'line.type', 'point.size', 'point.shape')
requireLength = c(2, 2, 2, 2)
default = list(NULL, NULL, NULL, NULL)
nullIsFine = c(rep(T,4))
}
for (i in 1:length(params)){
one_param = params[i]
if( length(get(one_param))!=requireLength[i]){
isNull = is.null(get(one_param))
if(isNull && nullIsFine[i]){}else{
warning(paste('Parameter', one_param, 'requires', requireLength[i],'elements,','but', length(get(one_param)),
'is supplied.','Default setting is used.'))
}
assign(one_param, default[[i]])
}
}
###1. pre-process the object: auto.imu
if(!is(object, "auto.imu") ){
stop('This function can only operate on auto.imu object.')
}
#what is num.sensor and ncols
num.sensor = object[[1]][[2]]$num.sensor
ncols = sum(num.sensor)
#what is freq
freq = object[[1]][[2]]$freq
#what is axis
if(num.sensor[1] == 0 || num.sensor[2] == 0){##only "Accelerometer"/only "Gyroscope"
axis = rep(0, ncols)
for(i in 1:ncols){
axis[i] = object[[i]][[2]]$axis
}
}else{#both
axis = rep(0, ncols/2)
for(i in 1:(ncols/2)){
axis[i] = object[[i]][[2]]$axis
}
}
#assume
obj.list = vector("list", ncols)
for(i in 1:ncols){
obj.list[[i]] = object[[i]][[2]]
######---------------------#######
#obj.list[[i]]$scales = obj.list[[i]]$scales/100
}
##begin: generate the data frame
total.len = 0
each.len = numeric(ncols)
for (i in 1:ncols){
each.len[i] = length(obj.list[[i]]$wv.empir)
total.len = total.len + each.len[i]
}
#Initialize empty data frame with right number of rows
obj = data.frame(scales = numeric(total.len),
emp = numeric(total.len),
low = numeric(total.len),
high = numeric(total.len),
theo = numeric(total.len),
axis = 'AXIS',
sensor = 'SENSOR', stringsAsFactors=FALSE)
if(num.sensor[2] == 0){ ## only "Gyroscope"
#put data into data frame
t = 1
for (i in 1:ncols){
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = axis[i],
sensor = "Gyroscope",
stringsAsFactors=FALSE)
t = t +d
}
}else if(num.sensor[1] == 0){ #only "Accelerometer"
#put data into data frame
t = 1
for (i in 1:ncols){
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = axis[i],
sensor = "Accelerometer",
stringsAsFactors=FALSE)
t = t +d
}
}else{ # both "Gyroscope" and "Accelerometer"
#put data into data frame
t = 1
for (i in 1:ncols){
if(i <= length(axis)){
temp.axis = axis[i]
temp.sensor = "Gyroscope"
}else{
temp.axis = axis[i-length(axis)]
temp.sensor = "Accelerometer"
}
d = each.len[i]
obj[t:(t+d-1),] = data.frame(scales = obj.list[[i]]$scales/freq, # freq conversion
emp = obj.list[[i]]$wv.empir,
low = obj.list[[i]]$ci.low,
high = obj.list[[i]]$ci.high,
theo = obj.list[[i]]$theo,
axis = temp.axis,
sensor = temp.sensor,
stringsAsFactors=FALSE)
t = t +d
}
}
#-----END OF DATA PROCESSING-------------------------
object = obj
###2. auto-select param
if(CI){
#default setting
#first WV, then CI
if(is.null(line.color)){
line.color = c("#003C7D", "#003C7D", "#F47F24")
}
if(is.null(line.type)){
line.type = c('solid', 'dotted', 'solid')
}
if(is.null(point.size)){
point.size = c(0, 0, 0)
}
if(is.null(point.shape)){
point.shape = c(20, 20, 1)
}
##legend.label
#if(is.null(legend.label)){
# legend.label = c(expression(paste("Empirical WV ", hat(nu))), expression(paste("CI(", hat(nu)," , 0.95)" )) )
#}
#change the length to meet the requirement of ggplot2
if(length(line.color) == 3){
line.color = c(line.color[1:2], line.color[2:3])
}
if(length(line.type) == 3){
line.type = c(line.type[1:2], line.type[2:3])
}
if(length(point.size) == 3){
point.size = c(point.size[1:2], point.size[2:3])
}
if(length(point.shape) == 3){
point.shape = c(point.shape[1:2], point.shape[2:3])
}
#breaks = c('WV','low')
#legend.fill = c(NA, alpha(CI.color,transparence) )
#legend.linetype = c(line.type[1],'blank' )
#legend.pointshape = c(point.shape[1], NA )
}else{
if(is.null(line.color)){
line.color = c("#003C7D", "#F47F24")
}
if(is.null(line.type)){
line.type = c('solid', 'solid')
}
if(is.null(point.size)){
point.size = c(0,0)
}
if(is.null(point.shape)){
point.shape = c(20, 1)
}
#if(is.null(legend.label)){
# legend.label = parse(text = c(expression(paste("Empirical WV ", hat(nu))) ) )
#}
#breaks = c('WV')
}
### 3.reconstruct data frame
#re-construct the data frame
if(CI){
obj = data.frame(scales = object$scales,
emp = object$emp,
low = object$low,
high = object$high,
theo = object$theo,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}else{
obj = data.frame(scales = object$scales,
emp = object$emp,
theo = object$theo,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
}
melt.obj = melt(obj, id.vars = c('scales', 'axis', 'sensor'))
### 4. start to plot
p = ggplot() +
#geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable), size = 1) +
geom_line(data = melt.obj, mapping = aes(x = scales, y = value, linetype = variable, color = variable)) +
geom_point(data = melt.obj, mapping = aes(x = scales, y = value, size = variable, shape = variable, color = variable)) +
scale_linetype_manual(values = c(line.type)) +
scale_shape_manual(values = c(point.shape))+
scale_size_manual(values = c(point.size)) +
scale_color_manual(values = c(line.color))
if(CI){
#construct the data frame to plot CI
obj.CI = data.frame(scales = object$scales,
low = object$low,
high = object$high,
axis = object$axis,
sensor = object$sensor, stringsAsFactors = F)
p = p +
geom_ribbon(data = obj.CI, mapping = aes(x = scales, ymin = low, ymax = high), fill = alpha(CI.color, transparence), show.legend = F)
# guides(colour = guide_legend(override.aes = list(fill = legend.fill, linetype = legend.linetype, shape = legend.pointshape)))
#CI.color: a hexadecimal color value
}
if( background == 'white'){
p = p + theme_bw()
}
p = p + theme(legend.position='none') + theme(strip.background = element_rect(fill= facet.label.background) )
p = p + facet_grid(sensor ~ axis, scales = scales) +
scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
xlab(axis.x.label) + ylab(axis.y.label) + ggtitle(title) +
theme(
plot.title = element_text(size= title.size),
axis.title.y = element_text(size= axis.label.size),
axis.text.y = element_text(size= axis.tick.size),
axis.title.x = element_text(size= axis.label.size),
axis.text.x = element_text(size= axis.tick.size),
#legend.key.size = unit(legend.key.size, "cm"),
#legend.text = element_text(size = legend.text.size),
#legend.title = element_text(size = legend.title.size),
#legend.background = element_rect(fill="transparent"),
#legend.text.align = 0,
strip.text = element_text(size = facet.label.size) )
p
}
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