R/plots.R
In pyCGM2/rCGM2:
Defines functions
geom_stdRibbon
geom_normative_ribbon
geom_vline_descriptiveEvents_bothContext
addGaitDescriptiveEventsLines
descriptivePlot_bothContext
consistencyPlot_bothContext
descriptivePlot
consistencyPlot
Documented in
addGaitDescriptiveEventsLines
consistencyPlot
consistencyPlot_bothContext
descriptivePlot
descriptivePlot_bothContext
geom_normative_ribbon
geom_stdRibbon
geom_vline_descriptiveEvents_bothContext
#' @title
#' consistencyPlot
#' @description
#' plot all cycle of a frame sequence
#' @param table [dataframe] all-cycle table
#' @param iLabel [string] label of the frame sequence
#' @param iEventContext [string] context of the frame sequence
#' @param iAxis [string] axis of the frame sequence
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @param colorFactor [string] line color according an independant variable
#' @param facetFactor [string] create \textit{facet} plot ( see ggplot2) for an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
consistencyPlot<-function(table, iEventContext , iLabel,iAxis,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL,
colorFactor=NULL,facetFactor=NULL,linetypeFactor=NULL){
gatherFramesTbl = table %>% gather(Frame, Values, Frame0:Frame100)
iData = filter(gatherFramesTbl,
Label == iLabel & Axis == iAxis & EventContext == iEventContext)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
iData$inter <- interaction(iData$Index) # !!!! I spent lot of time to find that
#iData$inter <- interaction(iData$Id,iData$Label,iData$EventContext,iData$Axis,iData$ComparisonFactor, iData$Cycle) # !!!! I spent lot of time to find that
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = colorFactor,
linetype = linetypeFactor,
group = "inter"),
size=0.5)
} else if ((!is.null(colorFactor)) && (is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = colorFactor,
group = "inter"),
size=0.5)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
linetype = linetypeFactor,
group = "inter"),
size=0.5)
} else {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = "EventContext",
group = "inter"),
size=0.5)
}
}
#' @title
#' descriptivePlot
#' @description
#' plot descriptive statistics of a frame sequence
#' @param descStatsFrameSequence [dataframe] descriptive stats table of frame sequence
#' @param iLabel [string] label of the frame sequence
#' @param iEventContext [string] context of the frame sequence
#' @param iAxis [string] axis of the frame sequence
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @param colorFactor [string] line color according an independant variable
#' @param facetFactor [string] create \textit{facet} plot ( see ggplot2) for an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param lineWidth [float] line width value
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
descriptivePlot<-function(descStatsFrameSequence, iEventContext , iLabel,iAxis,
iTitle="",yLabel="Deg", legendPosition = "none",
colorFactor=NULL,facetFactor=NULL,linetypeFactor=NULL,
ylimits=NULL,
lineWidth=0.5){
gatherFramesTbl = transform_frameData_descritiveStats(descStatsFrameSequence)
iData = filter(gatherFramesTbl,
Stats == "mean" &
Label == iLabel & Axis == iAxis & EventContext == iEventContext )
fig = ggplot() +
ggtitle(iTitle)+
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
iData$inter <- interaction(iData$Index) # !!!! I spent lot of time to find that
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = colorFactor,
linetype = linetypeFactor,
group = "inter"),
size=lineWidth)
} else if ((!is.null(colorFactor)) && (is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = colorFactor,
group = "inter"),
size=lineWidth)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
linetype = linetypeFactor,
group = "inter"),
size=lineWidth)
} else {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = "EventContext",
group = "inter"),
size=lineWidth)
if (iEventContext=="Left"){
fig = fig + scale_color_manual(values=c("red"))
} else if (iEventContext=="Right"){
fig = fig + scale_color_manual(values=c("blue"))
}
}
if (!is.null(facetFactor)){ fig = fig+facet_grid(paste0(".~", facetFactor))}
return(fig)
}
#' @title
#' consistencyPlot_bothContext
#' @description
#' plot all left and right cycles of a frame sequence
#' @param table [dataframe] all-cycle table
#' @param LabelLeft [string] label of the frame sequence for the left context
#' @param AxisLeft [string] axis of the frame sequence for the left context
#' @param LabelRight [string] label of the frame sequence for the right context
#' @param AxisRight [string] axis of the frame sequence for the Left context
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
consistencyPlot_bothContext<-function(table, LabelLeft,AxisLeft, LabelRight,AxisRight,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL){
gatherFramesTbl = table %>% gather(Frame, Values, Frame0:Frame100)
iData_L = filter(gatherFramesTbl,
Label == LabelLeft & Axis == AxisLeft)
iData_R = filter(gatherFramesTbl,
Label == LabelRight & Axis == AxisRight)
iData = bind_rows(iData_L, iData_R)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
fig = fig + geom_line(data=iData,
aes(x=Frame,y=Values,
color = EventContext,
group=interaction(Index)),
size=0.5)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
fig
return(fig)
}
#' @title
#' descriptivePlot_bothContext
#' @description
#' plot left and right descriptivestats of a frame sequence
#' @param descStatsFrameSequence [dataframe] descriptive stats table of frame sequence
#' @param LabelLeft [string] label of the frame sequence for the left context
#' @param AxisLeft [string] axis of the frame sequence for the left context
#' @param LabelRight [string] label of the frame sequence for the right context
#' @param AxisRight [string] axis of the frame sequence for the Left context
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
descriptivePlot_bothContext<-function(descStatsFrameSequence, LabelLeft,AxisLeft, LabelRight,AxisRight,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL){
gatherFramesTbl = gather_descriptiveStats_FrameSequences( descStatsFrameSequence)
iData_L = filter(gatherFramesTbl,
Stats == "mean" &
Label == LabelLeft & Axis == AxisLeft & EventContext == "Left" )
iData_R = filter(gatherFramesTbl,
Stats == "mean" &
Label == LabelRight & Axis == AxisRight & EventContext == "Right")
iData = bind_rows(iData_L, iData_R)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
fig = fig + geom_line(data=iData,
aes(x=Frame,y=Values,
color = EventContext,
group=interaction(Index)),
size=0.5)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
return(fig)
}
#---- figure add-on----
#' @title
#' addGaitDescriptiveEventsLines
#' @description
#' add gait events of a specific context as vertical lines to a figure
#' @param [fig] ggplot2 figure
#' @param [descStatsPhaseTable] descriptive stats table of gait phase scalar
#' (must include c("stancePhase","doubleStance1","doubleStance2")
#' @param [EventContext] selected context
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#'
#' @return []
#' @examples
#'
#' @section Warning:
#'
addGaitDescriptiveEventsLines<-function(fig,descStatsPhaseTable,iEventContext,
colorFactor=NULL,linetypeFactor=NULL ){
if ("ComparisonFactor" %ni% names(descStatsPhaseTable))
{
descStatsPhaseTable$ComparisonFactor = descStatsPhaseTable$EventContext
}
gaitEventsTableFilt = filter(descStatsPhaseTable, EventContext == iEventContext)
gaitEvents = transform_scalar_DescriptiveStats(gaitEventsTableFilt,STP)
gaitEvents = filter(gaitEvents, Stats == "mean" )
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color=colorFactor,
linetype = linetypeFactor),show_guide = FALSE)
} else if (!(is.null(colorFactor)) && (is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color=colorFactor),show_guide = FALSE)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
linetype=linetypeFactor),show_guide = FALSE)
} else {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color="EventContext"),show_guide = FALSE)
}
return(fig)
}
#' @title
#' addGaitDescriptiveEventsLines_bothContext
#' @description
#' add gait events from left and right context as vertical lines to a figure
#' @param [fig] ggplot2 figure
#' @param [descStatsPhaseTable] descriptive stats table of gait phases
#' (must include c("stancePhase","doubleStance1","doubleStance2")
#'
#' @return []
#' @examples
#'
#' @section Warning:
#'
geom_vline_descriptiveEvents_bothContext<-function(descStatsPhaseTable){
if ("ComparisonFactor" %ni% names(descStatsPhaseTable))
{
descStatsPhaseTable$ComparisonFactor = descStatsPhaseTable$EventContext
}
gaitEvents =gather_descritiveStats(descStatsPhaseTable,"ComparisonFactor",c("stancePhase","doubleStance1","doubleStance2"))
geom_vline( data = filter(gaitEvents,Factor == "stancePhase"),
aes(xintercept=Mean, color=ComparisonFactor))
}
#' @title
#' geom_normative_ribbon
#' @description
#' new ggplot2 geom displaying corridor of normative data
#' @param data [dataframe] normative data table
#' @return []
#' @examples
#'
#' @section Note:
#' programming as a new geom ( see https://rpubs.com/hadley/97970)
geom_normative_ribbon <- function(data) {
# programming as a new geom ( see https://rpubs.com/hadley/97970)
list(
geom_ribbon(data = data,
aes(ymin = Min, ymax = Max, x= Frame,group=interaction(Label,Axis)),
fill = "grey70",alpha = 0.4)
)
}
#' @title
#' geom_stdRibbon
#' @description
#' new ggplot2 geom displaying std corridor
#' @param table [dataframe] all cycle table
#' @return []
#' @examples
#'
#' @section Note:
#' programming as a new geom ( see https://rpubs.com/hadley/97970)
geom_stdRibbon <- function(table,bySubjectFlag) {
data = getStdCorridorLimits(table)
if ("ComparisonFactor" %ni% names(data))
{
data$ComparisonFactor =data$EventContext
}
geom_ribbon(data = data,
aes(ymin = Min, ymax = Max,fill = ComparisonFactor, x= Frame,group=interaction(ComparisonFactor,Label,Axis)),
alpha = 0.4)
}
pyCGM2/rCGM2 documentation built on July 28, 2020, 2:09 p.m.
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Defines functions geom_stdRibbon geom_normative_ribbon geom_vline_descriptiveEvents_bothContext addGaitDescriptiveEventsLines descriptivePlot_bothContext consistencyPlot_bothContext descriptivePlot consistencyPlot
Documented in addGaitDescriptiveEventsLines consistencyPlot consistencyPlot_bothContext descriptivePlot descriptivePlot_bothContext geom_normative_ribbon geom_stdRibbon geom_vline_descriptiveEvents_bothContext
#' @title
#' consistencyPlot
#' @description
#' plot all cycle of a frame sequence
#' @param table [dataframe] all-cycle table
#' @param iLabel [string] label of the frame sequence
#' @param iEventContext [string] context of the frame sequence
#' @param iAxis [string] axis of the frame sequence
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @param colorFactor [string] line color according an independant variable
#' @param facetFactor [string] create \textit{facet} plot ( see ggplot2) for an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
consistencyPlot<-function(table, iEventContext , iLabel,iAxis,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL,
colorFactor=NULL,facetFactor=NULL,linetypeFactor=NULL){
gatherFramesTbl = table %>% gather(Frame, Values, Frame0:Frame100)
iData = filter(gatherFramesTbl,
Label == iLabel & Axis == iAxis & EventContext == iEventContext)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
iData$inter <- interaction(iData$Index) # !!!! I spent lot of time to find that
#iData$inter <- interaction(iData$Id,iData$Label,iData$EventContext,iData$Axis,iData$ComparisonFactor, iData$Cycle) # !!!! I spent lot of time to find that
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = colorFactor,
linetype = linetypeFactor,
group = "inter"),
size=0.5)
} else if ((!is.null(colorFactor)) && (is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = colorFactor,
group = "inter"),
size=0.5)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
linetype = linetypeFactor,
group = "inter"),
size=0.5)
} else {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Values",
color = "EventContext",
group = "inter"),
size=0.5)
}
}
#' @title
#' descriptivePlot
#' @description
#' plot descriptive statistics of a frame sequence
#' @param descStatsFrameSequence [dataframe] descriptive stats table of frame sequence
#' @param iLabel [string] label of the frame sequence
#' @param iEventContext [string] context of the frame sequence
#' @param iAxis [string] axis of the frame sequence
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @param colorFactor [string] line color according an independant variable
#' @param facetFactor [string] create \textit{facet} plot ( see ggplot2) for an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#' @param lineWidth [float] line width value
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
#'
descriptivePlot<-function(descStatsFrameSequence, iEventContext , iLabel,iAxis,
iTitle="",yLabel="Deg", legendPosition = "none",
colorFactor=NULL,facetFactor=NULL,linetypeFactor=NULL,
ylimits=NULL,
lineWidth=0.5){
gatherFramesTbl = transform_frameData_descritiveStats(descStatsFrameSequence)
iData = filter(gatherFramesTbl,
Stats == "mean" &
Label == iLabel & Axis == iAxis & EventContext == iEventContext )
fig = ggplot() +
ggtitle(iTitle)+
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
iData$inter <- interaction(iData$Index) # !!!! I spent lot of time to find that
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = colorFactor,
linetype = linetypeFactor,
group = "inter"),
size=lineWidth)
} else if ((!is.null(colorFactor)) && (is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = colorFactor,
group = "inter"),
size=lineWidth)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))){
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
linetype = linetypeFactor,
group = "inter"),
size=lineWidth)
} else {
fig = fig + geom_line(data=iData,
aes_string(x="Frame",y="Value",
color = "EventContext",
group = "inter"),
size=lineWidth)
if (iEventContext=="Left"){
fig = fig + scale_color_manual(values=c("red"))
} else if (iEventContext=="Right"){
fig = fig + scale_color_manual(values=c("blue"))
}
}
if (!is.null(facetFactor)){ fig = fig+facet_grid(paste0(".~", facetFactor))}
return(fig)
}
#' @title
#' consistencyPlot_bothContext
#' @description
#' plot all left and right cycles of a frame sequence
#' @param table [dataframe] all-cycle table
#' @param LabelLeft [string] label of the frame sequence for the left context
#' @param AxisLeft [string] axis of the frame sequence for the left context
#' @param LabelRight [string] label of the frame sequence for the right context
#' @param AxisRight [string] axis of the frame sequence for the Left context
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
consistencyPlot_bothContext<-function(table, LabelLeft,AxisLeft, LabelRight,AxisRight,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL){
gatherFramesTbl = table %>% gather(Frame, Values, Frame0:Frame100)
iData_L = filter(gatherFramesTbl,
Label == LabelLeft & Axis == AxisLeft)
iData_R = filter(gatherFramesTbl,
Label == LabelRight & Axis == AxisRight)
iData = bind_rows(iData_L, iData_R)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
fig = fig + geom_line(data=iData,
aes(x=Frame,y=Values,
color = EventContext,
group=interaction(Index)),
size=0.5)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
fig
return(fig)
}
#' @title
#' descriptivePlot_bothContext
#' @description
#' plot left and right descriptivestats of a frame sequence
#' @param descStatsFrameSequence [dataframe] descriptive stats table of frame sequence
#' @param LabelLeft [string] label of the frame sequence for the left context
#' @param AxisLeft [string] axis of the frame sequence for the left context
#' @param LabelRight [string] label of the frame sequence for the right context
#' @param AxisRight [string] axis of the frame sequence for the Left context
#' @param iTitle [string] plot title
#' @param yLabel [string] label of the Y-axis
#' @param legendPosition [string] position of the legend (see legend.position of ggplot2)
#' @param ylimits [list] limits of the y-axis
#' @return fig [ggplot2 figure]
#' @examples
#'
#' @section Warning:
#'
descriptivePlot_bothContext<-function(descStatsFrameSequence, LabelLeft,AxisLeft, LabelRight,AxisRight,
iTitle="",yLabel="Deg", legendPosition = "none",
ylimits=NULL){
gatherFramesTbl = gather_descriptiveStats_FrameSequences( descStatsFrameSequence)
iData_L = filter(gatherFramesTbl,
Stats == "mean" &
Label == LabelLeft & Axis == AxisLeft & EventContext == "Left" )
iData_R = filter(gatherFramesTbl,
Stats == "mean" &
Label == LabelRight & Axis == AxisRight & EventContext == "Right")
iData = bind_rows(iData_L, iData_R)
fig = ggplot() +
scale_x_discrete(name="Time Normalized")+
ylab(yLabel)+#scale_y_continuous(name=yLabel)+
ggtitle(iTitle)+
theme(panel.grid.minor = element_blank(),
axis.title.x = element_text(size = 10),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size=8),
legend.text = element_text(size = 8),
legend.title = element_text(size = 10,face="plain"),
plot.title = element_text(family="Times", face="plain", size=10),
legend.position=legendPosition)
fig = fig + geom_line(data=iData,
aes(x=Frame,y=Values,
color = EventContext,
group=interaction(Index)),
size=0.5)
if (!is.null(ylimits)){ fig = fig + ylim(ylimits[1],ylimits[2])}
return(fig)
}
#---- figure add-on----
#' @title
#' addGaitDescriptiveEventsLines
#' @description
#' add gait events of a specific context as vertical lines to a figure
#' @param [fig] ggplot2 figure
#' @param [descStatsPhaseTable] descriptive stats table of gait phase scalar
#' (must include c("stancePhase","doubleStance1","doubleStance2")
#' @param [EventContext] selected context
#' @param colorFactor [string] line color according an independant variable
#' @param linetypeFactor [string] line type definied according an independant variable
#'
#' @return []
#' @examples
#'
#' @section Warning:
#'
addGaitDescriptiveEventsLines<-function(fig,descStatsPhaseTable,iEventContext,
colorFactor=NULL,linetypeFactor=NULL ){
if ("ComparisonFactor" %ni% names(descStatsPhaseTable))
{
descStatsPhaseTable$ComparisonFactor = descStatsPhaseTable$EventContext
}
gaitEventsTableFilt = filter(descStatsPhaseTable, EventContext == iEventContext)
gaitEvents = transform_scalar_DescriptiveStats(gaitEventsTableFilt,STP)
gaitEvents = filter(gaitEvents, Stats == "mean" )
if ((!is.null(colorFactor)) && (!is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color=colorFactor,
linetype = linetypeFactor),show_guide = FALSE)
} else if (!(is.null(colorFactor)) && (is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color=colorFactor),show_guide = FALSE)
} else if ((is.null(colorFactor)) && !(is.null(linetypeFactor))) {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
linetype=linetypeFactor),show_guide = FALSE)
} else {
fig = fig + geom_vline( data = filter(gaitEvents,Variable == "stancePhase"),
aes_string(xintercept="Value",
color="EventContext"),show_guide = FALSE)
}
return(fig)
}
#' @title
#' addGaitDescriptiveEventsLines_bothContext
#' @description
#' add gait events from left and right context as vertical lines to a figure
#' @param [fig] ggplot2 figure
#' @param [descStatsPhaseTable] descriptive stats table of gait phases
#' (must include c("stancePhase","doubleStance1","doubleStance2")
#'
#' @return []
#' @examples
#'
#' @section Warning:
#'
geom_vline_descriptiveEvents_bothContext<-function(descStatsPhaseTable){
if ("ComparisonFactor" %ni% names(descStatsPhaseTable))
{
descStatsPhaseTable$ComparisonFactor = descStatsPhaseTable$EventContext
}
gaitEvents =gather_descritiveStats(descStatsPhaseTable,"ComparisonFactor",c("stancePhase","doubleStance1","doubleStance2"))
geom_vline( data = filter(gaitEvents,Factor == "stancePhase"),
aes(xintercept=Mean, color=ComparisonFactor))
}
#' @title
#' geom_normative_ribbon
#' @description
#' new ggplot2 geom displaying corridor of normative data
#' @param data [dataframe] normative data table
#' @return []
#' @examples
#'
#' @section Note:
#' programming as a new geom ( see https://rpubs.com/hadley/97970)
geom_normative_ribbon <- function(data) {
# programming as a new geom ( see https://rpubs.com/hadley/97970)
list(
geom_ribbon(data = data,
aes(ymin = Min, ymax = Max, x= Frame,group=interaction(Label,Axis)),
fill = "grey70",alpha = 0.4)
)
}
#' @title
#' geom_stdRibbon
#' @description
#' new ggplot2 geom displaying std corridor
#' @param table [dataframe] all cycle table
#' @return []
#' @examples
#'
#' @section Note:
#' programming as a new geom ( see https://rpubs.com/hadley/97970)
geom_stdRibbon <- function(table,bySubjectFlag) {
data = getStdCorridorLimits(table)
if ("ComparisonFactor" %ni% names(data))
{
data$ComparisonFactor =data$EventContext
}
geom_ribbon(data = data,
aes(ymin = Min, ymax = Max,fill = ComparisonFactor, x= Frame,group=interaction(ComparisonFactor,Label,Axis)),
alpha = 0.4)
}
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