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Miscellaneous plot improvements #178

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2ccd318
Handle multiple subjects in plot_ranges.R
jwolfson Feb 26, 2025
911c505
Update plot_ranges.R documentation
jwolfson Feb 26, 2025
1d855b0
Improve format of 1-subject lasagna plots
jwolfson Feb 26, 2025
977d963
Improve multi-person lasagna_plots
jwolfson Feb 26, 2025
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209 changes: 151 additions & 58 deletions R/lasagna_plots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,9 @@ plot_lasagna_1subject <- function(data, lasagnatype = c('unsorted', 'timesorted'

id = glucose = day = NULL
rm(list = c("id", "glucose", "day"))

static_or_gui = match.arg(static_or_gui)

# Optionally convert data to log scale
if (log){
data$gl = log10(data$gl)
Expand All @@ -47,7 +47,7 @@ plot_lasagna_1subject <- function(data, lasagnatype = c('unsorted', 'timesorted'
LLTR = log10(LLTR)
ULTR = log10(ULTR)
}

# Select the color scheme
color_scheme = match.arg(color_scheme, c("blue-red", "red-orange"))
if (color_scheme == "blue-red"){
Expand All @@ -57,27 +57,27 @@ plot_lasagna_1subject <- function(data, lasagnatype = c('unsorted', 'timesorted'
# Alternative red and orange as in commercial software
colors = c("#8E1B1B", "#F92D00", "#48BA3C", "#F9F000", "#F9B500")
}

subject = unique(data$id)
ns = length(subject)
if (ns > 1){
subject = subject[1]
warning(paste("The provided data have", ns, "subjects. The plot will only be created for subject", subject))
data = data %>% dplyr::filter(id == subject)
}

# Get measurements on uniform grid from day to day
data_ip = CGMS2DayByDay(data, tz = tz, dt0 = dt0, inter_gap = inter_gap)
gl_by_id_ip = data_ip[[1]]
dt0 = data_ip$dt0
ndays = nrow(gl_by_id_ip)
ntimes = ncol(gl_by_id_ip)
time_grid_hours = cumsum(rep(dt0, 24 * 60 /dt0)) / 60

title = ""
ytitle = "Day"
xtitle = "Hour"

lasagnatype = match.arg(lasagnatype, c('unsorted', 'timesorted', 'daysorted'))
if (lasagnatype == 'timesorted'){
gl_by_id_ip = apply(gl_by_id_ip, 2, sort, decreasing = TRUE, na.last = TRUE)
Expand All @@ -88,33 +88,65 @@ plot_lasagna_1subject <- function(data, lasagnatype = c('unsorted', 'timesorted'
title = ", sorted within each day."
xtitle = "Hour (sorted)"
}

# Melt the measurements for lasagna plot
data_l = data.frame(day = rep(data_ip$actual_dates, each = ntimes), hour = rep(time_grid_hours, ndays), glucose = as.vector(t(gl_by_id_ip)))

# Make a plot
p = data_l %>%
ggplot(aes(x = hour, y = as.character(day), fill = glucose)) + scale_fill_gradientn(colors = colors, na.value = "grey50", values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])), limits = limits) + geom_tile() + ylab(ytitle) + ggtitle(paste0(subject, title, "")) + xlab(xtitle) + xlim(c(0, 24))

if(log){
p = p + ggplot2::labs(fill = 'log(glucose)')
}

# Take out days if sorted within time since each subject changes
if (lasagnatype == 'timesorted'){
p = p + theme(axis.text.y=element_blank())
data_l = data.frame(day = rep(data_ip$actual_dates, each = ntimes),
hour = rep(time_grid_hours, ndays),
glucose = as.vector(t(gl_by_id_ip))) %>%
mutate(tooltip_text = paste0(
"Day: ", day,
"<br>Hour: ", round(hour, 2),
if (!log) {
paste0("<br>Glucose (mg/dL): ", round(glucose, 1))
} else {
paste0("<br>Log10 Glucose: ", round(glucose, 2))
}
))

# Base ggplot
p <- ggplot(data_l, aes(
x = hour,
y = as.character(day),
fill = glucose,
text = tooltip_text # <- Important for Plotly
)) +
geom_tile() +
scale_fill_gradientn(
colors = colors,
na.value = "grey50",
values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])),
limits = limits,
name = if (!log) "Glucose (mg/dL)" else "log10(Glucose)"
) +
xlab(xtitle) +
ylab(ytitle) +
scale_x_continuous(limits = c(0, 24) + c(0, 0.05), expand = c(0, 0)) +
scale_y_discrete(expand = c(0, 0)) +
ggtitle(paste0(subject, title)) +
theme_bw() +
theme(
panel.background = element_rect(fill = "grey50"),
panel.grid.major = element_line(linewidth = 0, linetype = 'solid', colour = "grey50"),
panel.grid.minor = element_line(linewidth = 0, linetype = 'solid', colour = "grey50")
)

# If sorted within time, no meaningful day order
if (lasagnatype == 'timesorted') {
p <- p + theme(axis.text.y = element_blank())
}

p <- p + theme(panel.background = element_rect(fill = "grey50"),
panel.grid.major = element_line(linewidth=0, linetype = 'solid', colour = "grey50"),
panel.grid.minor = element_line(linewidth=0, linetype = 'solid', colour = "grey50")
)


# Return either static ggplot or interactive plotly
static_or_gui = match.arg(static_or_gui, c("plotly", "ggplot"))
if (static_or_gui == "plotly") {
return(plotly::ggplotly(p))
# Only show the text in the tooltip
return(
plotly::ggplotly(
p,
tooltip = "text"
)
)
}

return(p)
}

Expand Down Expand Up @@ -146,13 +178,13 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
maxd = 14, limits = c(50, 500), midpoint = 105, LLTR = 70, ULTR = 180, dt0 = NULL, inter_gap = 45, tz = "",
color_scheme = c("blue-red", "red-orange"), log = F, static_or_gui = c('ggplot', 'plotly')){

lasagnatype = match.arg(lasagnatype, c('unsorted', 'timesorted', 'subjectsorted'))
lasagnatype = match.arg(lasagnatype, c('unsorted', 'timesorted', 'subjectsorted'))
datatype = match.arg(datatype, c("all", "average"))
static_or_gui = match.arg(static_or_gui)

id = glucose = day = NULL
rm(list = c("id", "glucose", "day"))

# Optionally convert data to log scale
if (log){
data$gl = log10(data$gl)
Expand All @@ -161,10 +193,10 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
LLTR = log10(LLTR)
ULTR = log10(ULTR)
}

subject = unique(data$id)
ns = length(subject)

# Select the color scheme
color_scheme = match.arg(color_scheme, c("blue-red", "red-orange"))
if (color_scheme == "blue-red"){
Expand All @@ -174,7 +206,7 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
# Alternative red and orange as in commercial software
colors = c("#8E1B1B", "#F92D00", "#48BA3C", "#F9F000", "#F9B500")
}

# Calculate uniform grid for all subjects
gdall = list()
for (i in 1:ns){
Expand All @@ -187,13 +219,13 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
gdall[[i]] <- out$gd2d
}
dt0 = out$dt0

if (datatype == "average"){
# Combine the list of averages into the matrix form
average24 = t(sapply(gdall, colMeans, na.rm = TRUE))
# Time grid for 24 hour period
time_grid_hours = cumsum(rep(dt0, 24 * 60 /dt0)) / 60

# Adjust the title and sort if needed
title = ""
ytitle = "Subject"
Expand All @@ -207,27 +239,58 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
title = ", sorted within each subject."
xtitle = "Hour (sorted)"
}

# Melt the measurements for lasanga plot
data_l = data.frame(subject = rep(subject, each = length(time_grid_hours)), hour = rep(time_grid_hours, ns), glucose = as.vector(t(average24)))


# Melt the measurements for lasagna plot
data_l = data.frame(subject = rep(subject,
each = length(time_grid_hours)),
hour = rep(time_grid_hours, ns),
glucose = as.vector(t(average24))) %>%
mutate(tooltip_text = paste0(
"<br>Hour: ", round(hour, 2),
if (!log) {
paste0("<br>Glucose (mg/dL): ", round(glucose, 1))
} else {
paste0("<br>Log10 Glucose: ", round(glucose, 2))
}
))


p = data_l%>%
ggplot(aes(x = hour, y = subject, fill = glucose)) + geom_tile() + ylab(ytitle) + ggtitle(paste0("Average glucose values for all subjects across days", title, "")) + xlab(xtitle) + xlim(c(0, 24)) + scale_fill_gradientn(colors = colors, na.value = "grey50", values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])), limits = limits)

ggplot(aes(x = hour, y = subject, fill = glucose, text = tooltip_text)) +
geom_tile() +
ylab(ytitle) +
ggtitle(paste0("Average glucose values for all subjects across days", title, "")) +
xlab(xtitle) +
scale_x_continuous(limits = c(0, 24) + c(0, 0.05), expand = c(0, 0)) +
scale_y_discrete(expand = c(0, 0)) +
scale_fill_gradientn(colors = colors, na.value = "grey50", values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])), limits = limits)
ggtitle(paste0(subject, title)) +
theme_bw() +
theme(
panel.background = element_rect(fill = "grey50"),
panel.grid.major = element_line(linewidth = 0, linetype = 'solid', colour = "grey50"),
panel.grid.minor = element_line(linewidth = 0, linetype = 'solid', colour = "grey50"))


if(log){
p = p + ggplot2::labs(fill = 'log(glucose)')
}

# Take out subject names if sorted within time since each subject changes
if (lasagnatype == 'timesorted'){
p = p + theme(axis.text.y=element_blank())
}

static_or_gui = match.arg(static_or_gui, c("plotly", "ggplot"))
if (static_or_gui == "plotly") {
return(plotly::ggplotly(p))
return(
plotly::ggplotly(
p,
tooltip = "text"
)
)
}

return(p)
}else{
max_days = max(sapply(gdall, function(x) nrow(x)))
Expand All @@ -244,9 +307,9 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
as.vector(t(x[1:max_days, ]))
}
}

out = t(sapply(gdall, stretch_select))

# Adjust the title and sort if needed
title = ""
ytitle = "Subject"
Expand All @@ -260,26 +323,56 @@ plot_lasagna <- function(data, datatype = c("all", "average"), lasagnatype = c('
title = ", sorted within each subject."
xtitle = "Day (sorted)"
}

data_l = data.frame(subject = rep(subject, each = nt * max_days), day = rep(time_grid_days, ns), glucose = as.vector(t(out)))


data_l = data.frame(subject = rep(subject, each = nt * max_days),
day = rep(time_grid_days, ns),
glucose = as.vector(t(out))) %>%
mutate(tooltip_text = paste0(
"Day: ", round(day, 2),
if (!log) {
paste0("<br>Glucose (mg/dL): ", round(glucose, 1))
} else {
paste0("<br>Log10 Glucose: ", round(glucose, 2))
}
))

p = data_l%>%
ggplot(aes(x = day + 1, y = subject, fill = glucose)) + geom_tile() + ylab(ytitle) + ggtitle(paste0("All subjects", title)) + xlab(xtitle) + geom_vline(xintercept = c(1:max_days)) + scale_x_continuous(breaks = seq(1, max_days, by = 2)) + scale_fill_gradientn(colors = colors, na.value = "grey50", values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])), limits = limits)

ggplot(aes(x = day + 1, y = subject, fill = glucose, text = tooltip_text)) +
geom_tile() +
ylab(ytitle) +
ggtitle(paste0("All subjects", title)) +
xlab(xtitle) +
geom_vline(xintercept = c(1:max_days)) +
scale_x_continuous(breaks = seq(1, max_days, by = 2), expand = c(0,0)) +
scale_y_discrete(expand = c(0,0)) +
scale_fill_gradientn(colors = colors, na.value = "grey50", values = scales::rescale(c(limits[1], LLTR, midpoint, ULTR, limits[2])), limits = limits) +
theme_bw() +
theme(
panel.background = element_rect(fill = "grey50"),
panel.grid.major = element_line(linewidth = 0, linetype = 'solid', colour = "grey50"),
panel.grid.minor = element_line(linewidth = 0, linetype = 'solid', colour = "grey50")
)


if(log){
p = p + ggplot2::labs(fill = 'log(glucose)')
}

# Take out subject names if sorted within time since each subject changes
if (lasagnatype == 'timesorted'){
p = p + theme(axis.text.y=element_blank())
}

static_or_gui = match.arg(static_or_gui, c("plotly", "ggplot"))
if (static_or_gui == "plotly") {
return(plotly::ggplotly(p))
return(
plotly::ggplotly(
p,
tooltip = "text"
)
)
}

return(p)
}
}
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