Skip to content

PML 1.2 #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
xinyue-L wants to merge 1 commit into
base: master
Choose a base branch
from
Open

PML 1.2 #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
212 changes: 106 additions & 106 deletions R/act_plot.R
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,106 +1,106 @@
#' trelliscope auxillary function
#'
#' Plot day observations.
#'
#' @param id individual ID.
#' @param id_Nday the ith day observation of the individual.
#' @param act_ori day observation.
#' @param act_ind individual mean observation.
#' @param act_all global mean observation.
#' @param act_max the upper limit of activity (y-axis).
#' @param band smoothing band paramter.
#'
#' @keywords internal
#'
#' @return individual to day observations.

#### activity plot
act_plot <- function(id,id_Nday,act_ori,act_ind,act_all,act_max,band,ori=FALSE,lw=TRUE) {
timeOfDay <- function(num) {
hour <- floor(num/60)
min <- num - 60*hour
min <- paste(0,min,sep="")
min <- substr(min,nchar(min)-1,nchar(min))
return(paste(hour,":",min,sep=""))
}
timeOfDay <- Vectorize(timeOfDay,vectorize.args="num")
xtime <- timeOfDay(1:1440)

len <- length(act_ind)
xseq <- seq(24/len,24,by=24/len)
d <- band*len
lws <- function(x,ff) lowess(x[c((len-d+1):len,1:len,1:d)],f=ff,iter=1)$y[(d+1):(d+len)]
vec <- lws(act_ori,band)
vec_ind <- lws(act_ind,band)
vec_all <- lws(act_all,band)
#vec <- act_ori
title_name <- paste("ID = ",id," #Day = ",id_Nday,sep="")

if(lw==TRUE & ori==FALSE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori, color="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,vec,color="black",width=2,legend="activity lowess") %>%
ly_lines(xseq,vec_ind,width=2,color="blue",legend="individual mean lowess") %>%
ly_lines(xseq,vec_all,color="red",width=2,legend="global mean lowess") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else if (lw==TRUE & ori==TRUE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori, color="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,act_ind,width=2,color="blue",alpha=0.2,legend="individual mean") %>%
ly_lines(xseq,act_all,color="red",alpha=0.2,width=2,legend="global mean") %>%
ly_lines(xseq,vec,color="black",width=2,legend="activity lowess") %>%
ly_lines(xseq,vec_ind,width=2,color="blue",legend="individual mean lowess") %>%
ly_lines(xseq,vec_all,color="yellow",width=2,legend="global mean lowess") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else if(lw==FALSE & ori==TRUE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori,color ="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,act_ind,width=2,color="blue",alpha=0.2,legend="individual mean") %>%
ly_lines(xseq,act_all,color="red",alpha=0.2,width=2,legend="global mean") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else {
stop("Error: at least plot one of the original and lowess!")
}
}
#' trelliscope auxillary function
#'
#' Plot day observations.
#'
#' @param id individual ID.
#' @param id_Nday the ith day observation of the individual.
#' @param act_ori day observation.
#' @param act_ind individual mean observation.
#' @param act_all global mean observation.
#' @param act_max the upper limit of activity (y-axis).
#' @param band smoothing band paramter.
#'
#' @keywords internal
#'
#' @return individual to day observations.
#### activity plot
act_plot <- function(id,id_Nday,act_ori,act_ind,act_all,act_max,band,ori=FALSE,lw=TRUE) {
timeOfDay <- function(num) {
hour <- floor(num/60)
min <- num - 60*hour
min <- paste(0,min,sep="")
min <- substr(min,nchar(min)-1,nchar(min))
return(paste(hour,":",min,sep=""))
}
timeOfDay <- Vectorize(timeOfDay,vectorize.args="num")
xtime <- timeOfDay(1:1440)
len <- length(act_ind)
xseq <- seq(24/len,24,by=24/len)
d <- band*len
lws <- function(x,ff) lowess(x[c((len-d+1):len,1:len,1:d)],f=ff,iter=1)$y[(d+1):(d+len)]
vec <- lws(act_ori,band)
vec_ind <- lws(act_ind,band)
vec_all <- lws(act_all,band)
#vec <- act_ori
title_name <- paste("ID = ",id," #Day = ",id_Nday,sep="")
if(lw==TRUE & ori==FALSE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori, color="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,vec,color="black",width=2,legend="activity lowess") %>%
ly_lines(xseq,vec_ind,width=2,color="blue",legend="individual mean lowess") %>%
ly_lines(xseq,vec_all,color="red",width=2,legend="global mean lowess") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else if (lw==TRUE & ori==TRUE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori, color="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,act_ind,width=2,color="blue",alpha=0.2,legend="individual mean") %>%
ly_lines(xseq,act_all,color="red",alpha=0.2,width=2,legend="global mean") %>%
ly_lines(xseq,vec,color="black",width=2,legend="activity lowess") %>%
ly_lines(xseq,vec_ind,width=2,color="blue",legend="individual mean lowess") %>%
ly_lines(xseq,vec_all,color="yellow",width=2,legend="global mean lowess") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else if(lw==FALSE & ori==TRUE) {
rbokeh::figure(title=title_name,legend_location = "top_left",
width=600, height=300,
#xlab="Time of the Day", ylab="Activity Count",
xlim=c(0,24), ylim=c(0, max(c(act_max,act_ind,act_all))+50),
tools=c("pan","wheel_zoom","box_zoom","resize",
"box_select","reset","save","help")) %>%
#ly_points(xseq, act_ori,color ="black", size=1, hover= "Time @xtime", alpha=0.5) %>%
ly_lines(xseq,act_ori,color="black",alpha=0.2,legend=FALSE) %>%
ly_points(xseq,vec,color="white",size=2,alpha=0,
hover=data.frame(Time=xtime,Activity=floor(vec)),legend=FALSE) %>%
ly_lines(xseq,act_ind,width=2,color="blue",alpha=0.2,legend="individual mean") %>%
ly_lines(xseq,act_all,color="red",alpha=0.2,width=2,legend="global mean") %>%
x_axis(label="Time of the Day",
desired_num_ticks = 10, num_minor_ticks= 2) %>%
y_axis(label="Activity Count") %>%
theme_axis(which=c("x","y"),axis_label_text_font = "Helvetica",
axis_label_text_font_size = "12pt", axis_label_text_font_style = "normal") %>%
theme_title(text_font_size="12pt",text_font="Helvetica") %>%
theme_legend(label_text_font_size = "8pt")
} else {
stop("Error: at least plot one of the original and lowess!")
}
}
Loading