R/plotPanel.R
In pyCGM2/rCGM2:
Defines functions
descriptiveKineticGaitPanel_bothContext
descriptiveKineticGaitPanel
descriptiveKinematicGaitPanel_bothContext
descriptiveKinematicGaitPanel
Documented in
descriptiveKinematicGaitPanel
descriptiveKinematicGaitPanel_bothContext
descriptiveKineticGaitPanel
descriptiveKineticGaitPanel_bothContext
### GAIT PLOT PANEL ####
#' @title
#' descriptiveKinematicGaitPanel
#' @description
#' convenient descriptive plot panel of gait kinematics for a specific context
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param EventContext [string] context of the frame sequence
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @param manualLineType [list] manual line type ( see ggplot2 doc)
#' @param manualSizeType [float] manual line size ( see ggplot2 doc)
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKinematicGaitPanel<- function(descStatsFrameSequence,descStatsPhases, EventContext,
colorFactor=NULL, linetypeFactor=NULL,
normativeData=NULL,stdCorridorFlag=FALSE,
manualLineType=NULL,manualSizeType=NULL){
if (EventContext== "Left"){
prefixe = "L"
} else if (EventContext== "Right"){
prefixe = "R"
} else if (EventContext== "Overall"){
prefixe = ""}
# trace uni
Pelvis_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(0,60),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Pelvis_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"Y",
iTitle="Pelvic obliquity",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Pelvis_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"Z",
iTitle="Pelvis rotation",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"X",
iTitle="Hip flexion",yLabel="Deg", legendPosition="none",ylimits=c(-20,70),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"Y",
iTitle="Hip Abd",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"Z",
iTitle="Hip rot",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"X",
iTitle="Knee flexion",yLabel="Deg", legendPosition="none",ylimits=c(-15,75),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"Y",
iTitle="Knee Abd",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"Z",
iTitle="Knee rot",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"AnkleAngles"),"X",
iTitle="Ankle flexion",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"AnkleAngles"),"Y",
iTitle="Ankle eversion",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
FootProgress_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"FootProgressAngles"),"Z",
iTitle="Foot progression",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
if (!(is.null(descStatsPhases))){
Pelvis_X=addGaitDescriptiveEventsLines(Pelvis_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Pelvis_Y=addGaitDescriptiveEventsLines(Pelvis_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Pelvis_Z=addGaitDescriptiveEventsLines(Pelvis_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_X=addGaitDescriptiveEventsLines(Hip_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Y=addGaitDescriptiveEventsLines(Hip_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Z=addGaitDescriptiveEventsLines(Hip_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_X=addGaitDescriptiveEventsLines(Knee_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Y=addGaitDescriptiveEventsLines(Knee_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Z=addGaitDescriptiveEventsLines(Knee_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_X=addGaitDescriptiveEventsLines(Ankle_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Y=addGaitDescriptiveEventsLines(Ankle_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
FootProgress_Z=addGaitDescriptiveEventsLines(FootProgress_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
}
if (!(is.null(normativeData))){
Pelvis_X = Pelvis_X+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "X"))
Pelvis_Y = Pelvis_Y+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Y"))
Pelvis_Z = Pelvis_Z+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Z"))
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "Y"))
FootProgress_Z = FootProgress_Z+geom_normative_ribbon(filter(normativeData,Label=="FootProgressAngles" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
# Pelvis_X = Pelvis_X +
# geom_ribbon(data = filter(data,Label=="PelvisAngles" & Axis == "X"),
# aes(ymin = Min, ymax = Max,fill = ComparisonFactor, x= Frame,group=interaction(ComparisonFactor,Label,Axis)),
# alpha = 0.4)
Pelvis_X = Pelvis_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "X"))
Pelvis_Y = Pelvis_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "Y"))
Pelvis_Z = Pelvis_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "Z"))
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleAngles") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleAngles") & Axis == "Y"))
FootProgress_Z = FootProgress_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"FootProgressAngles") & Axis == "Z"))
}
if (!(is.null(manualLineType))){
Pelvis_X = Pelvis_X + scale_linetype_manual(values=manualLineType)
Pelvis_Y = Pelvis_Y + scale_linetype_manual(values=manualLineType)
Pelvis_Z = Pelvis_Z + scale_linetype_manual(values=manualLineType)
Hip_X = Hip_X + scale_linetype_manual(values=manualLineType)
Hip_Y = Hip_Y + scale_linetype_manual(values=manualLineType)
Hip_Z = Hip_Z + scale_linetype_manual(values=manualLineType)
Knee_X = Knee_X + scale_linetype_manual(values=manualLineType)
Knee_Y = Knee_Y + scale_linetype_manual(values=manualLineType)
Knee_Z = Knee_Z + scale_linetype_manual(values=manualLineType)
Ankle_X = Ankle_X + scale_linetype_manual(values=manualLineType)
Ankle_Y = Ankle_Y + scale_linetype_manual(values=manualLineType)
FootProgress_Z = FootProgress_Z + scale_linetype_manual(values=manualLineType)
}
if (!(is.null(manualSizeType))){
Pelvis_X = Pelvis_X + scale_size_manual(values=manualSizeType)
Pelvis_Y = Pelvis_Y + scale_size_manual(values=manualSizeType)
Pelvis_Z = Pelvis_Z + scale_size_manual(values=manualSizeType)
Hip_X = Hip_X + scale_size_manual(values=manualSizeType)
Hip_Y = Hip_Y + scale_size_manual(values=manualSizeType)
Hip_Z = Hip_Z + scale_size_manual(values=manualSizeType)
Knee_X = Knee_X + scale_size_manual(values=manualSizeType)
Knee_Y = Knee_Y + scale_size_manual(values=manualSizeType)
Knee_Z = Knee_Z + scale_size_manual(values=manualSizeType)
Ankle_X = Ankle_X + scale_size_manual(values=manualSizeType)
Ankle_Y = Ankle_Y + scale_size_manual(values=manualSizeType)
FootProgress_Z = FootProgress_Z + scale_size_manual(values=manualSizeType)
}
p1 = plot_grid(Pelvis_X, Pelvis_Y,Pelvis_Z,ncol=3)
p2 = plot_grid(Hip_X, Hip_Y,Hip_Z,ncol=3)
p3 = plot_grid(Knee_X, Knee_Y,Knee_Z,ncol=3)
p4 = plot_grid(Ankle_X, Ankle_Y,FootProgress_Z,ncol=3)
legend_shared <- get_legend(Pelvis_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1, p2,p3, p4,
legend_shared,
nrow = 5,rel_heights = c(1,1,1,1, .2))
fig
return(fig)
}
#' @title
#' descriptiveKinematicGaitPanel_bothContext
#' @description
#' convenient descriptive plot panel of gait kinematics for left and right contexts
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKinematicGaitPanel_bothContext<- function(descStatsFrameSequence,descStatsPhases=NULL,
normativeData=NULL,stdCorridorFlag=TRUE){
#
Pelvis_X = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","X", "RPelvisAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(0,60))
Pelvis_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","Y", "RPelvisAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Pelvis_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","Z", "RPelvisAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Hip_X = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","X", "RHipAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-20,70))
Hip_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","Y", "RHipAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Hip_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","Z", "RHipAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Knee_X = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","X", "RKneeAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-15,75))
Knee_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","Y", "RKneeAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Knee_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","Z", "RKneeAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Ankle_X = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleAngles","X", "RAnkleAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Ankle_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleAngles","Y", "RAnkleAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="top",ylimits=c(-30,30))
FootProgress_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LFootProgressAngles","Z", "RFootProgressAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
if (!(is.null(descStatsPhases))){
Pelvis_X = Pelvis_X+geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Pelvis_Y = Pelvis_Y+ geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Pelvis_Z= Pelvis_Z +geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_X= Hip_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_Y=Hip_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_Z=Hip_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_X=Knee_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_Y=Knee_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_Z=Knee_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Ankle_X=Ankle_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Ankle_Y=Ankle_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
FootProgress_Z=FootProgress_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
}
if (!(is.null(normativeData))){
Pelvis_X = Pelvis_X+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "X"))
Pelvis_Y = Pelvis_Y+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Y"))
Pelvis_Z = Pelvis_Z+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Z"))
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "Y"))
FootProgress_Z = FootProgress_Z+geom_normative_ribbon(filter(normativeData,Label=="FootProgressAngles" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Pelvis_X = Pelvis_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "X"))
Pelvis_Y = Pelvis_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "Y"))
Pelvis_Z = Pelvis_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "Z"))
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleAngles","RAnkleAngles") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleAngles","RAnkleAngles") & Axis == "Y"))
FootProgress_Z = FootProgress_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LFootProgressAngles","RFootProgressAngles") & Axis == "Z"))
}
p1 = plot_grid(Pelvis_X, Pelvis_Y,Pelvis_Z,ncol=3)
p2 = plot_grid(Hip_X, Hip_Y,Hip_Z,ncol=3)
p3 = plot_grid(Knee_X, Knee_Y,Knee_Z,ncol=3)
p4 = plot_grid(Ankle_X, Ankle_Y,FootProgress_Z,ncol=3)
legend_shared <- get_legend(Pelvis_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1, p2,p3, p4,
legend_shared,
nrow = 5,rel_heights = c(1,1,1,1, .2))
fig
return(fig)
}
#' @title
#' descriptiveKineticGaitPanel
#' @description
#' convenient descriptive plot panel of gait kinetics for a specific context
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param EventContext [string] context of the frame sequence
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @param manualLineType [list] manual line type ( see ggplot2 doc)
#' @param manualSizeType [float] manual line size ( see ggplot2 doc)
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKineticGaitPanel<- function(descStatsFrameSequence,descStatsPhases, EventContext,
colorFactor=NULL, linetypeFactor=NULL,
normativeData=NULL,stdCorridorFlag=FALSE,
manualLineType=NULL,manualSizeType=NULL){
if (EventContext== "Left"){
prefixe = "L"
} else if (EventContext== "Right"){
prefixe = "R"
} else if (EventContext== "Overall"){
prefixe = ""}
Hip_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"X",
iTitle="Hip extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"Y",
iTitle="Hip abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,2.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipPower"),"Z",
iTitle="Hip power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"X",
iTitle="Knee extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"Y",
iTitle="Knee abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneePower"),"Z",
iTitle="Knee power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"X",
iTitle="Ankle extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"Y",
iTitle="Ankle abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnklePower"),"Z",
iTitle="Ankle power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,5.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
if (!(is.null(descStatsPhases))){
Hip_X=addGaitDescriptiveEventsLines(Hip_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Y=addGaitDescriptiveEventsLines(Hip_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Z=addGaitDescriptiveEventsLines(Hip_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Power=addGaitDescriptiveEventsLines(Hip_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_X=addGaitDescriptiveEventsLines(Knee_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Y=addGaitDescriptiveEventsLines(Knee_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Z=addGaitDescriptiveEventsLines(Knee_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Power=addGaitDescriptiveEventsLines(Knee_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_X=addGaitDescriptiveEventsLines(Ankle_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Y=addGaitDescriptiveEventsLines(Ankle_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Z=addGaitDescriptiveEventsLines(Ankle_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Power=addGaitDescriptiveEventsLines(Ankle_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
}
if (!(is.null(normativeData))){
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Z"))
Hip_Power = Hip_Power+geom_normative_ribbon(filter(normativeData,Label=="HipPower" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Z"))
Knee_Power = Knee_Power+geom_normative_ribbon(filter(normativeData,Label=="KneePower" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Y"))
Ankle_Z = Ankle_Z+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Z"))
Ankle_Power = Ankle_Power+geom_normative_ribbon(filter(normativeData,Label=="AnklePower" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "Z"))
Hip_Power = Hip_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipPower") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "Z"))
Knee_Power = Knee_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneePower") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "Y"))
Ankle_Z = Ankle_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "Z"))
Ankle_Power = Ankle_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnklePower") & Axis == "Z"))
}
if (!(is.null(manualLineType))){
Hip_X = Hip_X + scale_linetype_manual(values=manualLineType)
Hip_Y = Hip_Y + scale_linetype_manual(values=manualLineType)
Hip_Z = Hip_Z + scale_linetype_manual(values=manualLineType)
Hip_Power = Hip_Power + scale_linetype_manual(values=manualLineType)
Knee_X = Knee_X + scale_linetype_manual(values=manualLineType)
Knee_Y = Knee_Y + scale_linetype_manual(values=manualLineType)
Knee_Z = Knee_Z + scale_linetype_manual(values=manualLineType)
Knee_Power = Knee_Power + scale_linetype_manual(values=manualLineType)
Ankle_X = Ankle_X + scale_linetype_manual(values=manualLineType)
Ankle_Y = Ankle_Y + scale_linetype_manual(values=manualLineType)
Ankle_Z = Ankle_Z + scale_linetype_manual(values=manualLineType)
Ankle_Power = Ankle_Power + scale_linetype_manual(values=manualLineType)
}
if (!(is.null(manualSizeType))){
Hip_X = Hip_X + scale_size_manual(values=manualSizeType)
Hip_Y = Hip_Y + scale_size_manual(values=manualSizeType)
Hip_Z = Hip_Z + scale_size_manual(values=manualSizeType)
Hip_Power = Hip_Power + scale_size_manual(values=manualSizeType)
Knee_X = Knee_X + scale_size_manual(values=manualSizeType)
Knee_Y = Knee_Y + scale_size_manual(values=manualSizeType)
Knee_Z = Knee_Z + scale_size_manual(values=manualSizeType)
Knee_Power = Knee_Power + scale_size_manual(values=manualSizeType)
Ankle_X = Ankle_X + scale_size_manual(values=manualSizeType)
Ankle_Y = Ankle_Y + scale_size_manual(values=manualSizeType)
Ankle_Z = Ankle_Z + scale_size_manual(values=manualSizeType)
Ankle_Power = Ankle_Power + scale_size_manual(values=manualSizeType)
}
p1 = plot_grid(Hip_X, Hip_Y,Hip_Z,Hip_power,ncol=4)
p2 = plot_grid(Knee_X, Knee_Y,Knee_Z,Knee_power,ncol=4)
p3 = plot_grid(Ankle_X, Ankle_Y,Ankle_Z,Ankle_power,ncol=4)
legend_shared <- get_legend(Hip_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1,p2,p3,legend_shared,
nrow = 4, rel_heights = c(1,1,1,.2))
fig
return(fig)
}
#' @title
#' descriptiveKineticGaitPanel_bothContext
#' @description
#' convenient descriptive plot panel of gait kinematics for left and right contexts
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKineticGaitPanel_bothContext<- function(descStatsFrameSequence,descStatsPhases=NULL,
normativeData=NULL,stdCorridorFlag=FALSE){
Hip_X = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","X", "RHipMoment","X",
iTitle="Hip extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,3.0))
Hip_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Y", "RHipMoment","Y",
iTitle="Hip abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,2.0))
Hip_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Z", "RHipMoment","Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Hip_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Z", "RHipMoment","Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0))
Knee_X = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","X", "RKneeMoment","X",
iTitle="Knee extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0))
Knee_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Y", "RKneeMoment","Y",
iTitle="Knee abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0))
Knee_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Z", "RKneeMoment","Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Knee_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Z", "RKneeMoment","Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0))
Ankle_X = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","X", "RAnkleMoment","X",
iTitle="Ankle extensor moment",yLabel="N.m.kg-1", legendPosition="top",ylimits=c(-1.0,3.0))
Ankle_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Y", "RAnkleMoment","Y",
iTitle="Ankle abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Ankle_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Z", "RAnkleMoment","Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Ankle_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Z", "RAnkleMoment","Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-5.0,5.0))
if (!(is.null(descStatsPhases))){
Hip_X=addGaitDescriptiveEventsLines_bothContext(Hip_X,descStatsPhases)
Hip_Y=addGaitDescriptiveEventsLines_bothContext(Hip_Y,descStatsPhases)
Hip_Z=addGaitDescriptiveEventsLines_bothContext(Hip_Z,descStatsPhases)
Hip_Power=addGaitDescriptiveEventsLines_bothContext(Hip_Power,descStatsPhases)
Knee_X=addGaitDescriptiveEventsLines_bothContext(Knee_X,descStatsPhases)
Knee_Y=addGaitDescriptiveEventsLines_bothContext(Knee_Y,descStatsPhases)
Knee_Z=addGaitDescriptiveEventsLines_bothContext(Knee_Z,descStatsPhases)
Knee_Power=addGaitDescriptiveEventsLines_bothContext(Knee_Power,descStatsPhases)
Ankle_X=addGaitDescriptiveEventsLines_bothContext(Ankle_X,descStatsPhases)
Ankle_Y=addGaitDescriptiveEventsLines_bothContext(Ankle_Y,descStatsPhases)
Ankle_Z=addGaitDescriptiveEventsLines_bothContext(Ankle_Z,descStatsPhases)
Ankle_Power=addGaitDescriptiveEventsLines_bothContext(Ankle_Power,descStatsPhases)
}
if (!(is.null(normativeData))){
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Z"))
Hip_Power = Hip_Power+geom_normative_ribbon(filter(normativeData,Label=="HipPower" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Z"))
Knee_Power = Knee_Power+geom_normative_ribbon(filter(normativeData,Label=="KneePower" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Y"))
Ankle_Z = Ankle_Z+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Z"))
Ankle_Power = Ankle_Power+geom_normative_ribbon(filter(normativeData,Label=="AnklePower" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "Z"))
Hip_Power = Hip_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipPower","RHipPower") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "Z"))
Knee_Power = Knee_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneePower","RKneePower") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "Y"))
Ankle_Z = Ankle_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "Z"))
Ankle_Power = Ankle_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnklePower","RAnklePower") & Axis == "Z"))
}
p1 = plot_grid(Hip_X, Hip_Y,Hip_Z,Hip_Power,ncol=4)
p2 = plot_grid(Knee_X, Knee_Y,Knee_Z,Knee_Power,ncol=4)
p3 = plot_grid(Ankle_X, Ankle_Y,Ankle_Z,Ankle_Power,ncol=4)
legend_shared <- get_legend(Hip_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1,p2,p3,legend_shared,
nrow = 4, rel_heights = c(1,1,1,.2))
fig
return(fig)
}
pyCGM2/rCGM2 documentation built on July 28, 2020, 2:09 p.m.
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Defines functions descriptiveKineticGaitPanel_bothContext descriptiveKineticGaitPanel descriptiveKinematicGaitPanel_bothContext descriptiveKinematicGaitPanel
Documented in descriptiveKinematicGaitPanel descriptiveKinematicGaitPanel_bothContext descriptiveKineticGaitPanel descriptiveKineticGaitPanel_bothContext
### GAIT PLOT PANEL ####
#' @title
#' descriptiveKinematicGaitPanel
#' @description
#' convenient descriptive plot panel of gait kinematics for a specific context
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param EventContext [string] context of the frame sequence
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @param manualLineType [list] manual line type ( see ggplot2 doc)
#' @param manualSizeType [float] manual line size ( see ggplot2 doc)
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKinematicGaitPanel<- function(descStatsFrameSequence,descStatsPhases, EventContext,
colorFactor=NULL, linetypeFactor=NULL,
normativeData=NULL,stdCorridorFlag=FALSE,
manualLineType=NULL,manualSizeType=NULL){
if (EventContext== "Left"){
prefixe = "L"
} else if (EventContext== "Right"){
prefixe = "R"
} else if (EventContext== "Overall"){
prefixe = ""}
# trace uni
Pelvis_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(0,60),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Pelvis_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"Y",
iTitle="Pelvic obliquity",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Pelvis_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"PelvisAngles"),"Z",
iTitle="Pelvis rotation",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"X",
iTitle="Hip flexion",yLabel="Deg", legendPosition="none",ylimits=c(-20,70),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"Y",
iTitle="Hip Abd",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"HipAngles"),"Z",
iTitle="Hip rot",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"X",
iTitle="Knee flexion",yLabel="Deg", legendPosition="none",ylimits=c(-15,75),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"Y",
iTitle="Knee Abd",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"KneeAngles"),"Z",
iTitle="Knee rot",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_X = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"AnkleAngles"),"X",
iTitle="Ankle flexion",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Y = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"AnkleAngles"),"Y",
iTitle="Ankle eversion",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
FootProgress_Z = descriptivePlot(descStatsFrameSequence, EventContext , paste0(prefixe,"FootProgressAngles"),"Z",
iTitle="Foot progression",yLabel="Deg", legendPosition="none",ylimits=c(-30,30),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
if (!(is.null(descStatsPhases))){
Pelvis_X=addGaitDescriptiveEventsLines(Pelvis_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Pelvis_Y=addGaitDescriptiveEventsLines(Pelvis_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Pelvis_Z=addGaitDescriptiveEventsLines(Pelvis_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_X=addGaitDescriptiveEventsLines(Hip_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Y=addGaitDescriptiveEventsLines(Hip_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Z=addGaitDescriptiveEventsLines(Hip_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_X=addGaitDescriptiveEventsLines(Knee_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Y=addGaitDescriptiveEventsLines(Knee_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Z=addGaitDescriptiveEventsLines(Knee_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_X=addGaitDescriptiveEventsLines(Ankle_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Y=addGaitDescriptiveEventsLines(Ankle_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
FootProgress_Z=addGaitDescriptiveEventsLines(FootProgress_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
}
if (!(is.null(normativeData))){
Pelvis_X = Pelvis_X+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "X"))
Pelvis_Y = Pelvis_Y+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Y"))
Pelvis_Z = Pelvis_Z+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Z"))
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "Y"))
FootProgress_Z = FootProgress_Z+geom_normative_ribbon(filter(normativeData,Label=="FootProgressAngles" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
# Pelvis_X = Pelvis_X +
# geom_ribbon(data = filter(data,Label=="PelvisAngles" & Axis == "X"),
# aes(ymin = Min, ymax = Max,fill = ComparisonFactor, x= Frame,group=interaction(ComparisonFactor,Label,Axis)),
# alpha = 0.4)
Pelvis_X = Pelvis_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "X"))
Pelvis_Y = Pelvis_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "Y"))
Pelvis_Z = Pelvis_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"PelvisAngles") & Axis == "Z"))
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipAngles") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeAngles") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleAngles") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleAngles") & Axis == "Y"))
FootProgress_Z = FootProgress_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"FootProgressAngles") & Axis == "Z"))
}
if (!(is.null(manualLineType))){
Pelvis_X = Pelvis_X + scale_linetype_manual(values=manualLineType)
Pelvis_Y = Pelvis_Y + scale_linetype_manual(values=manualLineType)
Pelvis_Z = Pelvis_Z + scale_linetype_manual(values=manualLineType)
Hip_X = Hip_X + scale_linetype_manual(values=manualLineType)
Hip_Y = Hip_Y + scale_linetype_manual(values=manualLineType)
Hip_Z = Hip_Z + scale_linetype_manual(values=manualLineType)
Knee_X = Knee_X + scale_linetype_manual(values=manualLineType)
Knee_Y = Knee_Y + scale_linetype_manual(values=manualLineType)
Knee_Z = Knee_Z + scale_linetype_manual(values=manualLineType)
Ankle_X = Ankle_X + scale_linetype_manual(values=manualLineType)
Ankle_Y = Ankle_Y + scale_linetype_manual(values=manualLineType)
FootProgress_Z = FootProgress_Z + scale_linetype_manual(values=manualLineType)
}
if (!(is.null(manualSizeType))){
Pelvis_X = Pelvis_X + scale_size_manual(values=manualSizeType)
Pelvis_Y = Pelvis_Y + scale_size_manual(values=manualSizeType)
Pelvis_Z = Pelvis_Z + scale_size_manual(values=manualSizeType)
Hip_X = Hip_X + scale_size_manual(values=manualSizeType)
Hip_Y = Hip_Y + scale_size_manual(values=manualSizeType)
Hip_Z = Hip_Z + scale_size_manual(values=manualSizeType)
Knee_X = Knee_X + scale_size_manual(values=manualSizeType)
Knee_Y = Knee_Y + scale_size_manual(values=manualSizeType)
Knee_Z = Knee_Z + scale_size_manual(values=manualSizeType)
Ankle_X = Ankle_X + scale_size_manual(values=manualSizeType)
Ankle_Y = Ankle_Y + scale_size_manual(values=manualSizeType)
FootProgress_Z = FootProgress_Z + scale_size_manual(values=manualSizeType)
}
p1 = plot_grid(Pelvis_X, Pelvis_Y,Pelvis_Z,ncol=3)
p2 = plot_grid(Hip_X, Hip_Y,Hip_Z,ncol=3)
p3 = plot_grid(Knee_X, Knee_Y,Knee_Z,ncol=3)
p4 = plot_grid(Ankle_X, Ankle_Y,FootProgress_Z,ncol=3)
legend_shared <- get_legend(Pelvis_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1, p2,p3, p4,
legend_shared,
nrow = 5,rel_heights = c(1,1,1,1, .2))
fig
return(fig)
}
#' @title
#' descriptiveKinematicGaitPanel_bothContext
#' @description
#' convenient descriptive plot panel of gait kinematics for left and right contexts
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKinematicGaitPanel_bothContext<- function(descStatsFrameSequence,descStatsPhases=NULL,
normativeData=NULL,stdCorridorFlag=TRUE){
#
Pelvis_X = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","X", "RPelvisAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(0,60))
Pelvis_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","Y", "RPelvisAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Pelvis_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LPelvisAngles","Z", "RPelvisAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Hip_X = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","X", "RHipAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-20,70))
Hip_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","Y", "RHipAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Hip_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LHipAngles","Z", "RHipAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Knee_X = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","X", "RKneeAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-15,75))
Knee_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","Y", "RKneeAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Knee_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeAngles","Z", "RKneeAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Ankle_X = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleAngles","X", "RAnkleAngles","X",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
Ankle_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleAngles","Y", "RAnkleAngles","Y",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="top",ylimits=c(-30,30))
FootProgress_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LFootProgressAngles","Z", "RFootProgressAngles","Z",
iTitle="Pelvic tilt",yLabel="Deg", legendPosition="none",ylimits=c(-30,30))
if (!(is.null(descStatsPhases))){
Pelvis_X = Pelvis_X+geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Pelvis_Y = Pelvis_Y+ geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Pelvis_Z= Pelvis_Z +geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_X= Hip_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_Y=Hip_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Hip_Z=Hip_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_X=Knee_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_Y=Knee_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Knee_Z=Knee_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Ankle_X=Ankle_X + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
Ankle_Y=Ankle_Y + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
FootProgress_Z=FootProgress_Z + geom_vline_descriptiveEvents_bothContext(descStatsPhases)
}
if (!(is.null(normativeData))){
Pelvis_X = Pelvis_X+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "X"))
Pelvis_Y = Pelvis_Y+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Y"))
Pelvis_Z = Pelvis_Z+geom_normative_ribbon(filter(normativeData,Label=="PelvisAngles" & Axis == "Z"))
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipAngles" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeAngles" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleAngles" & Axis == "Y"))
FootProgress_Z = FootProgress_Z+geom_normative_ribbon(filter(normativeData,Label=="FootProgressAngles" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Pelvis_X = Pelvis_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "X"))
Pelvis_Y = Pelvis_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "Y"))
Pelvis_Z = Pelvis_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LPelvisAngles","RPelvisAngles") & Axis == "Z"))
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipAngles","RHipAngles") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeAngles","RKneeAngles") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleAngles","RAnkleAngles") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleAngles","RAnkleAngles") & Axis == "Y"))
FootProgress_Z = FootProgress_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LFootProgressAngles","RFootProgressAngles") & Axis == "Z"))
}
p1 = plot_grid(Pelvis_X, Pelvis_Y,Pelvis_Z,ncol=3)
p2 = plot_grid(Hip_X, Hip_Y,Hip_Z,ncol=3)
p3 = plot_grid(Knee_X, Knee_Y,Knee_Z,ncol=3)
p4 = plot_grid(Ankle_X, Ankle_Y,FootProgress_Z,ncol=3)
legend_shared <- get_legend(Pelvis_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1, p2,p3, p4,
legend_shared,
nrow = 5,rel_heights = c(1,1,1,1, .2))
fig
return(fig)
}
#' @title
#' descriptiveKineticGaitPanel
#' @description
#' convenient descriptive plot panel of gait kinetics for a specific context
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param EventContext [string] context of the frame sequence
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @param manualLineType [list] manual line type ( see ggplot2 doc)
#' @param manualSizeType [float] manual line size ( see ggplot2 doc)
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKineticGaitPanel<- function(descStatsFrameSequence,descStatsPhases, EventContext,
colorFactor=NULL, linetypeFactor=NULL,
normativeData=NULL,stdCorridorFlag=FALSE,
manualLineType=NULL,manualSizeType=NULL){
if (EventContext== "Left"){
prefixe = "L"
} else if (EventContext== "Right"){
prefixe = "R"
} else if (EventContext== "Overall"){
prefixe = ""}
Hip_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"X",
iTitle="Hip extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"Y",
iTitle="Hip abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,2.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipMoment"),"Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Hip_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"HipPower"),"Z",
iTitle="Hip power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"X",
iTitle="Knee extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"Y",
iTitle="Knee abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneeMoment"),"Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Knee_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"KneePower"),"Z",
iTitle="Knee power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_X = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"X",
iTitle="Ankle extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,3.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Y = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"Y",
iTitle="Ankle abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Z = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnkleMoment"),"Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
Ankle_Power = descriptivePlot(descStatsFrameSequence, iSubjects, "Overall" , paste0(prefixe,"AnklePower"),"Z",
iTitle="Ankle power",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,5.0),
colorFactor = colorFactor,linetypeFactor = linetypeFactor, facetFactor = NULL)
if (!(is.null(descStatsPhases))){
Hip_X=addGaitDescriptiveEventsLines(Hip_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Y=addGaitDescriptiveEventsLines(Hip_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Z=addGaitDescriptiveEventsLines(Hip_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Hip_Power=addGaitDescriptiveEventsLines(Hip_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_X=addGaitDescriptiveEventsLines(Knee_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Y=addGaitDescriptiveEventsLines(Knee_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Z=addGaitDescriptiveEventsLines(Knee_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Knee_Power=addGaitDescriptiveEventsLines(Knee_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_X=addGaitDescriptiveEventsLines(Ankle_X,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Y=addGaitDescriptiveEventsLines(Ankle_Y,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Z=addGaitDescriptiveEventsLines(Ankle_Z,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
Ankle_Power=addGaitDescriptiveEventsLines(Ankle_Power,descStatsPhases,EventContext,
colorFactor=colorFactor, linetypeFactor=linetypeFactor )
}
if (!(is.null(normativeData))){
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Z"))
Hip_Power = Hip_Power+geom_normative_ribbon(filter(normativeData,Label=="HipPower" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Z"))
Knee_Power = Knee_Power+geom_normative_ribbon(filter(normativeData,Label=="KneePower" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Y"))
Ankle_Z = Ankle_Z+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Z"))
Ankle_Power = Ankle_Power+geom_normative_ribbon(filter(normativeData,Label=="AnklePower" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipMoment") & Axis == "Z"))
Hip_Power = Hip_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"HipPower") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneeMoment") & Axis == "Z"))
Knee_Power = Knee_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"KneePower") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "Y"))
Ankle_Z = Ankle_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnkleMoment") & Axis == "Z"))
Ankle_Power = Ankle_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label==paste0(prefixe,"AnklePower") & Axis == "Z"))
}
if (!(is.null(manualLineType))){
Hip_X = Hip_X + scale_linetype_manual(values=manualLineType)
Hip_Y = Hip_Y + scale_linetype_manual(values=manualLineType)
Hip_Z = Hip_Z + scale_linetype_manual(values=manualLineType)
Hip_Power = Hip_Power + scale_linetype_manual(values=manualLineType)
Knee_X = Knee_X + scale_linetype_manual(values=manualLineType)
Knee_Y = Knee_Y + scale_linetype_manual(values=manualLineType)
Knee_Z = Knee_Z + scale_linetype_manual(values=manualLineType)
Knee_Power = Knee_Power + scale_linetype_manual(values=manualLineType)
Ankle_X = Ankle_X + scale_linetype_manual(values=manualLineType)
Ankle_Y = Ankle_Y + scale_linetype_manual(values=manualLineType)
Ankle_Z = Ankle_Z + scale_linetype_manual(values=manualLineType)
Ankle_Power = Ankle_Power + scale_linetype_manual(values=manualLineType)
}
if (!(is.null(manualSizeType))){
Hip_X = Hip_X + scale_size_manual(values=manualSizeType)
Hip_Y = Hip_Y + scale_size_manual(values=manualSizeType)
Hip_Z = Hip_Z + scale_size_manual(values=manualSizeType)
Hip_Power = Hip_Power + scale_size_manual(values=manualSizeType)
Knee_X = Knee_X + scale_size_manual(values=manualSizeType)
Knee_Y = Knee_Y + scale_size_manual(values=manualSizeType)
Knee_Z = Knee_Z + scale_size_manual(values=manualSizeType)
Knee_Power = Knee_Power + scale_size_manual(values=manualSizeType)
Ankle_X = Ankle_X + scale_size_manual(values=manualSizeType)
Ankle_Y = Ankle_Y + scale_size_manual(values=manualSizeType)
Ankle_Z = Ankle_Z + scale_size_manual(values=manualSizeType)
Ankle_Power = Ankle_Power + scale_size_manual(values=manualSizeType)
}
p1 = plot_grid(Hip_X, Hip_Y,Hip_Z,Hip_power,ncol=4)
p2 = plot_grid(Knee_X, Knee_Y,Knee_Z,Knee_power,ncol=4)
p3 = plot_grid(Ankle_X, Ankle_Y,Ankle_Z,Ankle_power,ncol=4)
legend_shared <- get_legend(Hip_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1,p2,p3,legend_shared,
nrow = 4, rel_heights = c(1,1,1,.2))
fig
return(fig)
}
#' @title
#' descriptiveKineticGaitPanel_bothContext
#' @description
#' convenient descriptive plot panel of gait kinematics for left and right contexts
#' @param descStatsFrameSequence [dataframe] descriptive stats table of all frame sequences
#' @param descStatsPhases [dataframe] descriptive stats table of gait phase scalar ()
#' @param normativeData [dataframe] table of a normative dataset
#' @param stdCorridorFlag [Bool] add std corridor to plot
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
#'
descriptiveKineticGaitPanel_bothContext<- function(descStatsFrameSequence,descStatsPhases=NULL,
normativeData=NULL,stdCorridorFlag=FALSE){
Hip_X = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","X", "RHipMoment","X",
iTitle="Hip extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-2.0,3.0))
Hip_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Y", "RHipMoment","Y",
iTitle="Hip abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,2.0))
Hip_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Z", "RHipMoment","Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Hip_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LHipMoment","Z", "RHipMoment","Z",
iTitle="Hip rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0))
Knee_X = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","X", "RKneeMoment","X",
iTitle="Knee extensor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0))
Knee_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Y", "RKneeMoment","Y",
iTitle="Knee abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-1.0,1.0))
Knee_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Z", "RKneeMoment","Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Knee_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LKneeMoment","Z", "RKneeMoment","Z",
iTitle="Knee rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-3.0,3.0))
Ankle_X = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","X", "RAnkleMoment","X",
iTitle="Ankle extensor moment",yLabel="N.m.kg-1", legendPosition="top",ylimits=c(-1.0,3.0))
Ankle_Y = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Y", "RAnkleMoment","Y",
iTitle="Ankle abductor moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Ankle_Z = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Z", "RAnkleMoment","Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-0.5,0.5))
Ankle_Power = descriptivePlot_bothContext(descStatsFrameSequence, "LAnkleMoment","Z", "RAnkleMoment","Z",
iTitle="Ankle rotator moment",yLabel="N.m.kg-1", legendPosition="none",ylimits=c(-5.0,5.0))
if (!(is.null(descStatsPhases))){
Hip_X=addGaitDescriptiveEventsLines_bothContext(Hip_X,descStatsPhases)
Hip_Y=addGaitDescriptiveEventsLines_bothContext(Hip_Y,descStatsPhases)
Hip_Z=addGaitDescriptiveEventsLines_bothContext(Hip_Z,descStatsPhases)
Hip_Power=addGaitDescriptiveEventsLines_bothContext(Hip_Power,descStatsPhases)
Knee_X=addGaitDescriptiveEventsLines_bothContext(Knee_X,descStatsPhases)
Knee_Y=addGaitDescriptiveEventsLines_bothContext(Knee_Y,descStatsPhases)
Knee_Z=addGaitDescriptiveEventsLines_bothContext(Knee_Z,descStatsPhases)
Knee_Power=addGaitDescriptiveEventsLines_bothContext(Knee_Power,descStatsPhases)
Ankle_X=addGaitDescriptiveEventsLines_bothContext(Ankle_X,descStatsPhases)
Ankle_Y=addGaitDescriptiveEventsLines_bothContext(Ankle_Y,descStatsPhases)
Ankle_Z=addGaitDescriptiveEventsLines_bothContext(Ankle_Z,descStatsPhases)
Ankle_Power=addGaitDescriptiveEventsLines_bothContext(Ankle_Power,descStatsPhases)
}
if (!(is.null(normativeData))){
Hip_X = Hip_X+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "X"))
Hip_Y = Hip_Y+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Y"))
Hip_Z = Hip_Z+geom_normative_ribbon(filter(normativeData,Label=="HipMoment" & Axis == "Z"))
Hip_Power = Hip_Power+geom_normative_ribbon(filter(normativeData,Label=="HipPower" & Axis == "Z"))
Knee_X = Knee_X+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "X"))
Knee_Y = Knee_Y+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Y"))
Knee_Z = Knee_Z+geom_normative_ribbon(filter(normativeData,Label=="KneeMoment" & Axis == "Z"))
Knee_Power = Knee_Power+geom_normative_ribbon(filter(normativeData,Label=="KneePower" & Axis == "Z"))
Ankle_X = Ankle_X+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "X"))
Ankle_Y = Ankle_Y+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Y"))
Ankle_Z = Ankle_Z+geom_normative_ribbon(filter(normativeData,Label=="AnkleMoment" & Axis == "Z"))
Ankle_Power = Ankle_Power+geom_normative_ribbon(filter(normativeData,Label=="AnklePower" & Axis == "Z"))
}
if (stdCorridorFlag){
data = getStdCorridorLimits_fromDescStatFrameSequences(descStatsFrameSequence)
Hip_X = Hip_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "X"))
Hip_Y = Hip_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "Y"))
Hip_Z = Hip_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipMoment","RHipMoment") & Axis == "Z"))
Hip_Power = Hip_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LHipPower","RHipPower") & Axis == "Z"))
Knee_X = Knee_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "X"))
Knee_Y = Knee_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "Y"))
Knee_Z = Knee_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneeMoment","RKneeMoment") & Axis == "Z"))
Knee_Power = Knee_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LKneePower","RKneePower") & Axis == "Z"))
Ankle_X = Ankle_X + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "X"))
Ankle_Y = Ankle_Y + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "Y"))
Ankle_Z = Ankle_Z + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnkleMoment","RAnkleMoment") & Axis == "Z"))
Ankle_Power = Ankle_Power + geom_stdRibbon(filter(descStatsFrameSequence,Label %in% c("LAnklePower","RAnklePower") & Axis == "Z"))
}
p1 = plot_grid(Hip_X, Hip_Y,Hip_Z,Hip_Power,ncol=4)
p2 = plot_grid(Knee_X, Knee_Y,Knee_Z,Knee_Power,ncol=4)
p3 = plot_grid(Ankle_X, Ankle_Y,Ankle_Z,Ankle_Power,ncol=4)
legend_shared <- get_legend(Hip_X + theme(legend.position=c(0.3,0.8),legend.direction = "horizontal"))
fig = plot_grid(p1,p2,p3,legend_shared,
nrow = 4, rel_heights = c(1,1,1,.2))
fig
return(fig)
}
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