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actoplot_v6.R
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source("/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/DAM1_reader.R")
actoplot = function(file1 = file1,
file_format = "dam1", #"dam2", "ethoscope"
#y = activity, #name of column in datatable you want to display on y-axis
type_of_plot = "bar", #can be "bar", "line", "ribbon" or "tile"
num_of_plot = 2, #can be any integer
#operation = mean, #can be sum/median ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
operation = "mean", ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
#DD_days = NULL, #range of days that were in DD, e.g. LD = 0:2 for days 0 to 2 ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
DD_days_start = "none", #for sake of website, can't use NULL ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
DD_days_end = "none", ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
#LD_days = NULL, #range of days that were in LD, e.g. LD = 0:2 for days 0 to 2 ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
LD_days_start = "none", ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
LD_days_end = "none", ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
D_start = 0,
D_end_L_start = 12,
L_end = 24,
LD_offset = 0, #how much you want to shift the LD annotations by
condition = NULL,
#pop_overview = NULL, #if not null, then can choose which operation like above to further summarise the population data
pop_overview = "mean", ##REMINDER CHANGE THIS BACK FOR NON WEBSITE
time_to_round = rethomics:::hours(1) #see if can rename this to something used before
){
num_of_plot = as.numeric(num_of_plot)
if (num_of_plot%%1!=0){
stop("num_of_plot must be an integer")
}
if (file_format == "dam1"){
dt = copy(as.data.table(file1))
t_round = floor(dt[,t]/(time_to_round))
x_vals = (t_round%%(days(1)/time_to_round))
day = (floor(dt[,t]/(rethomics::days(1))))
dt[, t_round := t_round]
dt[, x_vals := x_vals]
dt[, day := day]
setkeyv(dt, c("experiment_id", "region_id", "date", "machine_name"))
if (operation == "mean"){
operation = mean
} else if (operation == "median"){
operation = median
} else if (operation == "sum"){
operation = sum
}
if (pop_overview == "mean"){
pop_overview = mean
} else if (pop_overview == "median"){
pop_overview = median
} else if (pop_overview == "sum"){
pop_overview = sum
} else if (pop_overview == "NULL"){
pop_overview = NULL
}
# if (condition == "moving"){
# condition = moving
# }
if (DD_days_start == "none"||DD_days_end == "none"){
DD_days = NULL
} else {
DD_days = DD_days_start:DD_days_end
}
if (LD_days_start == "none"||LD_days_end == "none"){
LD_days = NULL
} else {
LD_days = LD_days_start:LD_days_end
}
DD = DD_days
LD = LD_days
offset = LD_offset
if (length(unique(dt[,experiment_id])) == 1){
dt = dt[,.(experiment_id = experiment_id,
condition = condition,
machine_name = machine_name,
region_id = region_id,
date = date,
t=t,
activity = operation(activity),
x_vals = x_vals,
day = day),
by = t_round]
dt = unique(dt)
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(dt)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + (days(1)/time_to_round)]
dt = dt[day<(max(day))]
dt = rbind(dt, dt_temp)
dt = unique(dt)
}
}
dt = dt[day>-1]
dt = dt[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(12*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(dt, aes(x=x_vals, y=activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)", breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"),
plot.title = element_text(hjust = 0.5, size = 18),
axis.text.x = element_text(size=16),
axis.text.y = element_text(size=10),
axis.title=element_text(size=14,face="bold"),
strip.text = element_text(face="bold", size=14)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "line"){
p = ggplot(dt, aes(x_vals, activity)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "ribbon"){
p = ggplot(dt, aes(x_vals, ymin=min(activity), ymax=activity)) +
geom_ribbon() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "tile"){
dt[,row_name:=sprintf("%s | %02d",experiment_id,region_id)]
p = ggplot(dt,aes(x=x_vals,y=row_name,fill=activity)) +
geom_tile(alpha=1) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
labs(title="Overview of individual activity pattern over time",x="time", y="activity") +
guides(fill=guide_legend(title="activity"))
}
} else if (length(unique(dt[,experiment_id])) > 1){
summary_dt = dt[,list(activity=operation(activity),
x_vals=x_vals,
day=day),
by=c("t_round", key(dt), "condition")]
summary_dt = unique(summary_dt)
setkeyv(summary_dt, c("experiment_id", "date", "machine_name"))
summary_dt_all_animals = summary_dt[,list(activity=operation(activity)),
by=c("t_round", #see if can utilize key(dt)
key(summary_dt),
"condition",
"x_vals",
"day")]
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(summary_dt_all_animals)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + (days(1)/time_to_round)]
summary_dt_all_animals = summary_dt_all_animals[day<(max(day))]
summary_dt_all_animals = rbind(summary_dt_all_animals, dt_temp)
summary_dt_all_animals = unique(summary_dt_all_animals)
}
}
if (!is.null(pop_overview)){
summary_dt_all_animals = summary_dt_all_animals[,list(activity=pop_overview(activity)),
by=c("t_round",
"x_vals",
"day")]
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(8*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(summary_dt_all_animals, aes(x_vals, activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "line"){
p = ggplot(summary_dt_all_animals, aes(x_vals, activity)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "ribbon"){
p = ggplot(summary_dt_all_animals, aes(x_vals, ymin=min(activity), ymax=activity)) +
geom_ribbon() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "tile"){
summary_dt_all_animals[,row_name:=""]
p = ggplot(summary_dt_all_animals, aes(x=x_vals, y=row_name, fill=activity)) +
geom_tile(alpha=1) +
facet_grid(day_str ~ ., switch = "y") +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5), axis.ticks.y = element_blank()) +
labs(title="Overview Actogram plot of population activity over time",x="time", y="") #+
#guides(fill=guide_legend(title="activity"))
}
} else if (is.null(pop_overview)){
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(8*num_of_plot) * 6
p = ggplot(summary_dt_all_animals, aes(x_vals, activity, colour=machine_name)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Actogram plot of population activity over time")
# if (is.null(condition)){
# p = ggplot(summary_dt_all_animals, aes(x_vals, activity, colour=machine_name)) +
# geom_line() +
# facet_grid(day_str ~ .) +
# scale_x_continuous(name="time (hours)",breaks = x_scale) +
# scale_y_continuous(name="activity") +
# theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
# ggtitle("Actogram plot of population activity over time")
# } else if (!is.null(condition)){
# p = ggplot(summary_dt_all_animals, aes(x_vals, activity, colour=condition)) +
# geom_line() +
# facet_grid(day_str ~ .) +
# scale_x_continuous(name="time (hours)",breaks = x_scale) +
# scale_y_continuous(name="activity") +
# theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
# ggtitle("Actogram plot of population activity over time")
# }
}
}
} else if (file_format == "dam2"){
dt = copy(as.data.table(file1))
t_round = floor(dt[,t]/(time_to_round))
x_vals = t_round%%24
day = (floor(t_round/(24)))
dt[, t_round := t_round]
dt[, x_vals := x_vals]
dt[, day := day]
# setkeyv(dt, c("experiment_id", "region_id", "start_date", "machine_name"))
if (operation == "mean"){
operation = mean
} else if (operation == "median"){
operation = median
} else if (operation == "sum"){
operation = sum
}
if (pop_overview == "mean"){
pop_overview = mean
} else if (pop_overview == "median"){
pop_overview = median
} else if (pop_overview == "sum"){
pop_overview = sum
}
if (DD_days_start == "none"||DD_days_end == "none"){
DD_days = NULL
} else {
DD_days = DD_days_start:DD_days_end
}
if (LD_days_start == "none"||LD_days_end == "none"){
LD_days = NULL
} else {
LD_days = LD_days_start:LD_days_end
}
LD = LD_days
DD = DD_days
offset = LD_offset
if (length(unique(dt[,region_id])) == 1){
dt = dt[,list(activity=operation(activity),
x_vals=x_vals,
day=day),
by=c("t_round", key(dt))]
dt = unique(dt)
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(dt)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + 24]
dt = dt[day<(max(day))]
dt = rbind(dt, dt_temp)
dt = unique(dt)
}
}
dt = dt[day>-1]
dt = dt[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(4*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(dt, aes(x=x_vals, y=activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "line"){
p = ggplot(dt, aes(x_vals, activity)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "ribbon"){
p = ggplot(dt, aes(x_vals, ymin=min(activity), ymax=activity)) +
geom_ribbon() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "tile"){
dt[,row_name:=sprintf("%s | %02d",experiment_id,region_id)]
p = ggplot(dt,aes(x=x_vals,y=row_name,fill=activity)) +
geom_tile(alpha=1) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
labs(title="Overview of individual activity pattern over time",x="time", y="activity") +
guides(fill=guide_legend(title="activity"))
}
} else if (length(unique(dt[,region_id])) > 1) {
summary_dt = dt[,list(activity=operation(activity), #perform operation by t_round, i.e.average activity per hour
x_vals=x_vals,
day=day),
by=c("t_round", key(dt))]
summary_dt = unique(summary_dt)
setkeyv(summary_dt, c("experiment_id", "start_date", "stop_date", "machine_name"))
summary_dt_all_animals = summary_dt[,list(activity=operation(activity)),
by=c("t_round",
key(summary_dt),
"x_vals",
"day")]
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(summary_dt_all_animals)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + 24]
summary_dt_all_animals = summary_dt_all_animals[day<(max(day))]
summary_dt_all_animals = rbind(summary_dt_all_animals, dt_temp)
summary_dt_all_animals = unique(summary_dt_all_animals)
}
}
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(4*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(summary_dt_all_animals, aes(x_vals, activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "line"){
p = ggplot(summary_dt_all_animals, aes(x_vals, activity)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "ribbon"){
p = ggplot(summary_dt_all_animals, aes(x_vals, ymin=min(activity), ymax=activity)) +
geom_ribbon() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (type_of_plot == "tile"){
summary_dt_all_animals[,row_name:=""]
p = ggplot(summary_dt_all_animals, aes(x=x_vals, y=row_name, fill=activity)) +
geom_tile(alpha=1) +
facet_grid(day_str ~ ., switch = "y") +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5), axis.ticks.y = element_blank()) +
labs(title="Overview Actogram plot of population activity over time",x="time", y="") #+
#guides(fill=guide_legend(title="activity"))
}
}
} else if (file_format == "ethoscope"){
dt = copy(as.data.table(file1))
to.replace <- names(which(sapply(dt, is.logical)))
for (var in to.replace) dt[, var:= as.numeric(get(var)), with=FALSE]
t_round = floor(dt[,t]/(time_to_round))
x_vals = (t_round%%(days(1)/time_to_round))
day = (floor(dt[,t]/(rethomics::days(1))))
dt[, t_round := t_round]
dt[, x_vals := x_vals]
dt[, day := day]
#c_var_name <- deparse(substitute(condition))
c_var_name = condition
print(c_var_name)
if(c_var_name == "NULL")
dt[,c_var:=TRUE]
else
setnames(dt, c_var_name,"c_var")
setkeyv(dt, c("experiment_id", "region_id", "date", "machine_name"))
if (operation == "mean"){
operation = mean
} else if (operation == "median"){
operation = median
} else if (operation == "sum"){
operation = sum
}
if (pop_overview == "mean"){
pop_overview = mean
} else if (pop_overview == "median"){
pop_overview = median
} else if (pop_overview == "sum"){
pop_overview = sum
} else if (pop_overview == "NULL"){
pop_overview = NULL
}
if (DD_days_start == "none"||DD_days_end == "none"){
DD_days = NULL
} else {
DD_days = DD_days_start:DD_days_end
}
if (LD_days_start == "none"||LD_days_end == "none"){
LD_days = NULL
} else {
LD_days = LD_days_start:LD_days_end
}
DD = DD_days
LD = LD_days
offset = LD_offset
print(length(unique(dt[,region_id])))
if (length(unique(dt[,region_id])) == 1){
dt = dt[,.(experiment_id = experiment_id,
machine_name = machine_name,
region_id = region_id,
date = date,
t=t,
y_vals = operation(c_var),
x_vals = x_vals,
day = day),
by = t_round]
dt = unique(dt)
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(dt)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + (days(1)/time_to_round)]
dt = dt[day<(max(day))]
dt = rbind(dt, dt_temp)
dt = unique(dt)
}
}
dt = dt[day>-1]
dt = dt[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(12*num_of_plot) * 6
p = ggplot(dt, aes(x=x_vals, y=y_vals, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
x_max1 = (max(x_vals)+1)*num_of_plot
}
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)", breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"),
plot.title = element_text(hjust = 0.5, size = 18),
axis.text.x = element_text(size=16),
axis.text.y = element_text(size=10),
axis.title=element_text(size=14,face="bold"),
strip.text = element_text(face="bold", size=14)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (length(unique(dt[,region_id])) > 1){
summary_dt = dt[,list(y_vals=operation(c_var),
x_vals=x_vals,
day=day),
by=c("t_round", key(dt))]
summary_dt = unique(summary_dt)
setkeyv(summary_dt, c("experiment_id", "date", "machine_name"))
summary_dt_all_animals = summary_dt[,list(y_vals=operation(y_vals)),
by=c("t_round", #see if can utilize key(dt)
key(summary_dt),
"x_vals",
"day")]
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(summary_dt_all_animals)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + (days(1)/time_to_round)]
summary_dt_all_animals = summary_dt_all_animals[day<(max(day))]
summary_dt_all_animals = rbind(summary_dt_all_animals, dt_temp)
summary_dt_all_animals = unique(summary_dt_all_animals)
}
}
if (!is.null(pop_overview)){
summary_dt_all_animals = summary_dt_all_animals[,list(y_vals=pop_overview(y_vals)),
by=c("t_round",
"x_vals",
"day")]
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(8*num_of_plot) * 6
p = ggplot(summary_dt_all_animals, aes(x_vals, y_vals, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Overview Actogram plot of population activity over time")
} else if (is.null(pop_overview)){
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(8*num_of_plot) * 6
p = ggplot(summary_dt_all_animals, aes(x_vals, y_vals, colour=machine_name)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle("Actogram plot of population activity over time")
}
}
}
p
# if (length(unique(dt[,experiment_id])) == 1){
# return(dt)
# } else if (length(unique(dt[,experiment_id])) > 1){
# return(summary_dt_all_animals)
# }
}
##DAM1##
dam1 = DAM1_single_reader("/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/120115A5M/120115A5mCtM007C03.txt")
#dam1 = DAM1_single_reader("/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/Estaban_new_data/Circadian_data_for_Nicholas/220914es5/220914es5CtM011C27.txt")
PATH1 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/120115A5M"
PATH2 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/120115C5M"
PATH3 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/190115Aes"
PATH4 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/190115Bes"
PATH5 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/per_rescue_v2/190115Ces"
#dammulti1 = DAM1_multi_reader(PATH1, time_format = "min")
#dammulti2 = DAM1_multi_reader(PATH2, time_format = "min")
#dammulti3 = DAM1_multi_reader(PATH3, time_format = "min")
#dammulti4 = DAM1_multi_reader(PATH4, time_format = "min")
#dammulti5 = DAM1_multi_reader(PATH5, time_format = "min")
#dammulti = rbind(dammulti1, dammulti2)
# acto = actoplot_dam1(dammulti1,
# num_of_plot = 4,
# type_of_plot = "bar", #currently only "bar" has LD and DD annotations available
# #DD_days = NULL, #range of days that were in DD, e.g. LD = 0:2 for days 0 to 2
# DD_days_start = 7, #for website functionality
# DD_days_end = 4, #for website functionality
# #LD_days = 0:2,
# LD_days_start = 0,
# LD_days_end = 2,
# LD_offset = 0,
# D_start = 0,
# D_end_L_start = 12,
# L_end = 24,
# operation = "mean",
# pop_overview = "mean",
# time_to_round = hours(1))
# acto
##DAM2##
#file1 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/Anne_DAM2_Data/2015-08-05_M002_merged.txt"
#file1 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/Anne_DAM2_Data/2015-08-05_M010_merged.txt"
file1 = "/media/nick/Data/Users/N/Documents/MSc_Bioinfo/2016/Data_Analysis_Project/Circadian_Rhythm/Anne_DAM2_Data/2016-11-20_M012_merged.txt"
query = data.table(path=file1,
start_date="2016-11-21_00-00-00",
stop_date="2016-12-07",
#region_id=c(1:32),
region_id=c(2:32),
machine_name = "M012")
dam2 = loadDAM2Data(query)
#dam2 = rethomics:::loadSingleDAM2File(file1)
# library(chron)
# library(lubridate)
actoplot_dam2 = function(file1,
type_of_plot = "bar", #can be "bar", "line", "ribbon" or "tile"
num_of_plot = 2, #can be any integer
#mean = FALSE #change to actually use a function
operation = mean, #can be sum/median
DD_days = NULL, #range of days that were in DD, e.g. LD = 0:2 for days 0 to 2
LD_days = NULL, #range of days that were in LD, e.g. LD = 0:2 for days 0 to 2
LD_offset = NULL, #how much you want to shift the LD annotations by
D_start = 0,
D_end_L_start = 12,
L_end = 24,
#pop_overview = NULL, #if not null, then can choose which operation like above to further summarise the population data
time_to_round = rethomics:::hours(1) #see if can rename this to something used before
){
num_of_plot = as.numeric(num_of_plot)
if (num_of_plot%%1!=0){
stop("num_of_plot must be an integer")
}
# if (is.null(machine_name)){
# stop('"machine_name" must be specified')
# }
dt = copy(as.data.table(file1))
t_round = floor(dt[,t]/(time_to_round))
x_vals = t_round%%24
day = (floor(t_round/(24)))
dt[, t_round := t_round]
dt[, x_vals := x_vals]
dt[, day := day]
# setkeyv(dt, c("experiment_id", "region_id", "start_date", "machine_name"))
LD = LD_days
DD = DD_days
offset = LD_offset
if (length(unique(dt[,region_id])) == 1){
dt = dt[,list(activity=operation(activity),
x_vals=x_vals,
day=day),
by=c("t_round", key(dt))]
dt = unique(dt)
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(dt)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + 24]
dt = dt[day<(max(day))]
dt = rbind(dt, dt_temp)
dt = unique(dt)
}
}
dt = dt[day>-1]
dt = dt[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(4*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(dt, aes(x=x_vals, y=activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)
#ii = ii + (max(x_vals)+1)
ii = ii + L_end
}
}
if (!is.null(DD)){
p = p +
geom_rect(data=subset(dt, day_str == sprintf("day\n%03d", DD)), aes(fill=day_str), fill="grey", color="grey",size=0,xmin = 0,xmax = (max(x_vals)+1)*num_of_plot,ymin = -Inf,ymax = Inf,alpha = 1)
}
p = p +
geom_col(position = position_nudge(x = 0.5)) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "line"){
p = ggplot(dt, aes(x_vals, activity)) +
geom_line() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "ribbon"){
p = ggplot(dt, aes(x_vals, ymin=min(activity), ymax=activity)) +
geom_ribbon() +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
scale_y_continuous(name="activity") +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
ggtitle(sprintf("Actogram plot of individual activity over time of experiment %s", unique(dt[,experiment_id])))
} else if (type_of_plot == "tile"){
dt[,row_name:=sprintf("%s | %02d",experiment_id,region_id)]
p = ggplot(dt,aes(x=x_vals,y=row_name,fill=activity)) +
geom_tile(alpha=1) +
facet_grid(day_str ~ .) +
scale_x_continuous(name="time (hours)",breaks = x_scale) +
theme(panel.spacing = unit(0.2, "lines"), plot.title = element_text(hjust = 0.5)) +
labs(title="Overview of individual activity pattern over time",x="time", y="activity") +
guides(fill=guide_legend(title="activity"))
}
} else if (length(unique(dt[,region_id])) > 1) {
summary_dt = dt[,list(activity=operation(activity), #perform operation by t_round, i.e.average activity per hour
x_vals=x_vals,
day=day),
by=c("t_round", key(dt))]
summary_dt = unique(summary_dt)
setkeyv(summary_dt, c("experiment_id", "start_date", "stop_date", "machine_name"))
summary_dt_all_animals = summary_dt[,list(activity=operation(activity)),
by=c("t_round",
key(summary_dt),
"x_vals",
"day")]
if (num_of_plot>1){
for (i in 2:num_of_plot){
dt_temp = copy(summary_dt_all_animals)
dt_temp = dt_temp[, day := day-1]
dt_temp = dt_temp[, x_vals := x_vals + 24]
summary_dt_all_animals = summary_dt_all_animals[day<(max(day))]
summary_dt_all_animals = rbind(summary_dt_all_animals, dt_temp)
summary_dt_all_animals = unique(summary_dt_all_animals)
}
}
summary_dt_all_animals = summary_dt_all_animals[day>-1]
summary_dt_all_animals = summary_dt_all_animals[, day_str := sprintf("day\n%03d", day)]
x_scale = 0:(4*num_of_plot) * 6
if (type_of_plot == "bar"){
p = ggplot(summary_dt_all_animals, aes(x_vals, activity, width=1))
if (!is.null(LD)){
ii=0
a=1
for (i in 0:(num_of_plot+1)){
#print(ii)
x_min1 = D_start + ii + offset
x_max1 = D_end_L_start + ii + offset
#x_min2 = L_start + ii + offset
x_min2 = D_end_L_start + ii + offset
x_max2 = L_end + ii + offset
cat("MAXHOUR", max(x_vals), (max(x_vals)+1)*num_of_plot, "\n")
if (x_min1 < 0){
x_min1 = 0
}
if (x_min1 > ((max(x_vals)+1)*num_of_plot)){
a = 0
}
if (x_max1 < 0){
x_max1 = 0
}
if (x_max1 > ((max(x_vals)+1)*num_of_plot)){
print("yes")
x_max1 = (max(x_vals)+1)*num_of_plot
print(x_max1)
}
cat("x_m values", x_min1, x_max1, x_min2, x_max2, "\n")
p = p +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min1,
xmax = x_max1, ymin = -Inf,ymax = Inf,alpha = a) +
geom_rect(data=subset(summary_dt_all_animals, day_str == sprintf("day\n%03d", LD)), aes(fill=day_str), fill="grey", color="grey",size=0,
xmin = x_min2,
xmax = x_max2, ymin = -Inf,ymax = Inf,alpha = 0)