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replace invalid data bar by hashed area to make it easier to spot
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@vincentvanhees
vincentvanhees committed Jul 18, 2024
1 parent 84f1066 commit 8525afd
Showing 1 changed file with 56 additions and 48 deletions.
104 changes: 56 additions & 48 deletions R/visualreport.R
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,17 @@ visualreport = function(metadatadir = c(),
}
lev = lev + 1
}
if ("invalidepoch" %in% binary_vars) {
freqtab = table(mdat$invalidepoch)
if (length(freqtab) > 1 || names(freqtab)[1] == "1") {
t0 = mdat$timestamp[which(diff(c(0, mdat$invalidepoch)) == 1)]
t1 = mdat$timestamp[which(diff(c(mdat$invalidepoch, 0)) == -1)]
col = myred
rect(xleft = t0, xright = t1, ybottom = 0, ytop = Ymax,
col = col, density = 20, border = FALSE)
}
}

# onset/wake lines:
window_edges = which(diff(mdat$SleepPeriodTime) != 0)
if (length(window_edges) > 0) {
Expand Down Expand Up @@ -146,15 +157,18 @@ visualreport = function(metadatadir = c(),
if (length(freqtab) > 1 || names(freqtab)[1] == "1") {
t0 = mdat$timestamp[which(diff(c(0, mdat[,binary_vars[labi]])) == 1)]
t1 = mdat$timestamp[which(diff(c(mdat[, binary_vars[labi]], 0)) == -1)]
y0 = yticks[lev] + buffer
y1 = yticks[lev] - buffer
if (binary_vars[labi] == "invalidepoch") {
col = myred
rect(xleft = t0, xright = t1, ybottom = -Ymax, ytop = Ymax,
col = col, density = 20, border = FALSE)
} else {
y0 = yticks[lev] + buffer
y1 = yticks[lev] - buffer
col = mygreys[lev]
rect(xleft = t0, xright = t1, ybottom = y0, ytop = y1 , col = col, border = FALSE)
}
# print(paste0("y for rect bi: ", y0, " ", y1))
rect(xleft = t0, xright = t1, ybottom = y0, ytop = y1 , col = col, border = FALSE)

}
lev = lev + 1
}
Expand All @@ -176,7 +190,6 @@ visualreport = function(metadatadir = c(),
expected_ms5raw_path = paste0(metadatadir, "/meta/ms5.outraw")

if (dir.exists(expected_ts_path)) {

fnames.ms5raw = dir(expected_ts_path, pattern = "[.]RData")
N_ts_files = length(fnames.ms5raw)
if (f1 > N_ts_files) f1 = N_ts_files # this is intentionally ms3 and not ms4, do not change!
Expand Down Expand Up @@ -225,57 +238,52 @@ visualreport = function(metadatadir = c(),
ylabels_plot2 = gsub(pattern = "nap", replacement = "diary_nap", x = ylabels_plot2)
ylabels_plot2 = gsub(pattern = "nonwear", replacement = "diary_nonwear", x = ylabels_plot2)
ylabels_plot2 = gsub(pattern = "sleeplog", replacement = "diary_sleepwindow", x = ylabels_plot2)

# loop through files
for (i in f0:f1) {
# browser()
load(file = paste0(metadatadir, "/meta/ms5.outraw/",
part6_threshold_combi, "/", fnames.ms5raw[i]))

if (length(grep(pattern = "2405CH01_053891_2022-06-08 09-37-25", x = fnames.ms5raw[i], ignore.case = TRUE)) > 0) {
load(file = paste0(metadatadir, "/meta/ms5.outraw/",
part6_threshold_combi, "/", fnames.ms5raw[i]))
if (length(mdat) == 0) next
if (nrow(mdat) == 0) next

if (all(c("lightpeak", "selfreported", "sibdetection") %in% colnames(mdat))) {
simple_filename = gsub(pattern = ".RData", replacement = "", x = fnames.ms5raw[i] ) #"patientID12345"
pdf(paste0(metadatadir, "/results/file summary reports/Time_report_",
simple_filename, ".pdf"), paper = "a4",
width = 0, height = 0)
# zoom on windows that have either daytime sib or selfreported nap
acc_naps = which((mdat$sibdetection == 1 | mdat$selfreport == "nap") &
mdat$SleepPeriodTime == 0)


midnightsi = which(format(mdat$timestamp, "%H") == "00" &
format(mdat$timestamp, "%M") == "00" &
format(mdat$timestamp, "%S") == "00")
subploti = c(1, midnightsi + 1)
subploti = cbind(subploti,
c(midnightsi + 720, nrow(mdat)))

if (length(mdat) == 0) next
if (nrow(mdat) == 0) next
invalid = which(mdat$invalidepoch == 1)
# Skip windows without naps?
# for (jj in 1:nrow(subploti)) {
# ma = which(acc_naps > subploti[jj, 1] & acc_naps < subploti[jj, 2])
# if (length(ma) == 0) {
# is.na(subploti[jj, ]) = TRUE
# }
# }
subploti[which(subploti[,2] > nrow(mdat)), 2] = nrow(mdat)

if (all(c("lightpeak", "selfreported", "sibdetection") %in% colnames(mdat))) {
simple_filename = gsub(pattern = ".RData", replacement = "", x = fnames.ms5raw[i] ) #"patientID12345"
pdf(paste0(metadatadir, "/results/file summary reports/Time_report_",
simple_filename, ".pdf"), paper = "a4",
width = 0, height = 0)
# zoom on windows that have either daytime sib or selfreported nap
acc_naps = which((mdat$sibdetection == 1 | mdat$selfreport == "nap") &
mdat$SleepPeriodTime == 0)


midnightsi = which(format(mdat$timestamp, "%H") == "00" &
format(mdat$timestamp, "%M") == "00" &
format(mdat$timestamp, "%S") == "00")
subploti = c(1, midnightsi + 1)
subploti = cbind(subploti,
c(midnightsi + 720, nrow(mdat)))

invalid = which(mdat$invalidepoch == 1)
# Skip windows without naps?
# for (jj in 1:nrow(subploti)) {
# ma = which(acc_naps > subploti[jj, 1] & acc_naps < subploti[jj, 2])
# if (length(ma) == 0) {
# is.na(subploti[jj, ]) = TRUE
# }
# }
subploti[which(subploti[,2] > nrow(mdat)), 2] = nrow(mdat)

NdaysPerPage = 7
par(mfrow = c(NdaysPerPage * 2, 1), mgp = c(2, 0.8, 0), omi = c(0, 0, 0, 0), bty = "n")
if (nrow(subploti) > 0) {
for (ani in 1:nrow(subploti)) {

panelplot(mdat[(subploti[ani, 1] + 1):subploti[ani, 2], ],
ylabels_plot2, Nlevels, selfreport_vars, binary_vars,
BCN, BCC, title = "", dayid = ani)
}
NdaysPerPage = 7
par(mfrow = c(NdaysPerPage * 2, 1), mgp = c(2, 0.8, 0), omi = c(0, 0, 0, 0), bty = "n")
if (nrow(subploti) > 0) {
for (ani in 1:nrow(subploti)) {

panelplot(mdat[(subploti[ani, 1] + 1):subploti[ani, 2], ],
ylabels_plot2, Nlevels, selfreport_vars, binary_vars,
BCN, BCC, title = "", dayid = ani)
}
dev.off()
}
dev.off()
}
}
}
Expand Down

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