-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path3Graphing Script.R
579 lines (493 loc) · 40.1 KB
/
3Graphing Script.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
library(dplyr)
library(tidyverse)
graphcgm <- function(input,
output = tempdir(), metadata,
tz = "Australia/Sydney",
yaxis = c(0,20)){
# Get list of all CGM data files
files <- base::list.files(path = input,full.names = TRUE)
# Create a data frame to combine indiviudal CGM values into one dataf rame
aggregatecgm <- base::data.frame(matrix(ncol = 6,nrow = 0))
colnames(aggregatecgm) <- c("subjectid","timestamp","sglucose", "cgmperiod", "week", "studyid")
# Run through the input directory, combine all data.
for (f in 1:length(files)) {
cgmdata <-
utils::read.csv(files[f],stringsAsFactors = FALSE,header = TRUE,skipNul = TRUE)
id <- cgmdata$studyid[1]
cgmdata$subjectid <- id
aggregatecgm <- rbind(cgmdata,aggregatecgm)
}
aggregatecgm$sglucose <- as.numeric(aggregatecgm$sglucose) #convert glucose levels to numeric
## read in metadata (study arm and diabetic status for stratification)
## here, we read in clinical metadata that is used as a graphing variable. The metadata included columns named study_id, which we use later to join with the aggregatecgm dataframe
metadata <- read.csv("metadata/metadata.csv", header = TRUE, stringsAsFactors = TRUE)
metadata[,c(5:6)] <- lapply(metadata[,c(5:6)], factor) #convert columns from integer to factors
metadata <- metadata[,c(1,5,6)] #keep only the necessary columns
metadata <- metadata %>% tidyr::drop_na() #remove patients that were not randomised to a study arm (i.e screened but not enroled)
metadata$study_id <- as.numeric(metadata$study_id) #convert study id to numeric
metadata$study_id <- sprintf("%02d", as.numeric(metadata$study_id)) # add a leading "0" to study ids
metadata$study_id <- paste0("DIG", metadata$study_id) # add DIG prefix to study id
aggregatecgm <- left_join(aggregatecgm, metadata, by = c("studyid" = "study_id"))
# Remove rows which contain missing values
aggregatecgm <- aggregatecgm[stats::complete.cases(aggregatecgm),]
write.csv(aggregatecgm, "aggregatecgm.csv")
# Remove dates, so aggregated CGM data can be ordered by time of day
dateparseorder <- c("mdy HM","mdy HMS","mdY HM","mdY HMS","dmy HM","dmy HMS",
"dmY HM","dmY HMS","Ymd HM","Ymd HMS","ymd HM","ymd HMS",
"Ydm HM","Ydm HMS","ydm HM","ydm HMS")
aggregatecgm$timestamp <-
as.POSIXct(lubridate::parse_date_time(aggregatecgm$timestamp,
dateparseorder,tz = "Australia/Sydney")) ## convert timestamp data to time format
aggregatecgm$hour <- lubridate::round_date(aggregatecgm$timestamp,"hour") ## round time to the nearest hour
aggregatecgm$time <-
as.POSIXct(strftime(aggregatecgm$timestamp,format = "%H:%M", tz = "Australia/Sydney"),
format = "%H:%M") #remove date specifier, keep just the time
aggregatecgm$hourmin <-
lubridate::round_date(aggregatecgm$timestamp,"10 minutes") #remove date specifier, round the time to the nearest 10 minute mark
aggregatecgm$hourmin <-
as.POSIXct(strftime(aggregatecgm$hourmin,format = "%H:%M", tz = "Australia/Sydney"),
format = "%H:%M") # convert to time format
lims <- as.POSIXct(strptime(c("00:00","24:00"),format = "%H:%M")) ## set x-axis limits for graphs
target <- c(3.9, 10) ##target range for glucose measurements
range<- as.POSIXct(strptime(c("00:00"),format = "%H:%M")) ## lovation of "target range"
## Graphing using ggplot
# New facet label names for supp variable
week.labs <- c("Week 3", "Week 4", "Week 7", "Week 8")
names(week.labs) <- c("1", "2", "3", "4")
## Individual average CGM, faceted by week
for(i in unique(aggregatecgm$studyid)){
gi<- ggplot2::ggplot(aes(x = time, y = sglucose), data = subset(aggregatecgm, studyid == i))+
ggplot2::geom_smooth(aes(y = sglucose), method="loess", colour = "blue", se = FALSE)+
ggplot2::geom_point(ggplot2::aes(y = sglucose),shape =".")+
ggplot2::geom_ribbon(aes(ymin=3.9, ymax=10, fill="Target Range"), fill="skyblue", alpha=0.5, show.legend = TRUE)+
ggplot2::labs(title = "Daily Overlay Per Subject (loess Smoothing)", subtitle = (as.character(i)))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5), legend.position = "none")+
ggplot2::theme(axis.text.x = element_text(face="plain", color="black", size=7, angle=45))+
ggplot2::theme(axis.text.y = element_text(face="plain", color="black", size=7, angle=0))+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), limits = lims, expand=c(0.07,1)) +
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="dashed")+ ## horizontal lines for target glucose values >3.9 & < 10
ggplot2::scale_y_continuous(breaks = sort(c(seq(min(aggregatecgm$sglucose), max(aggregatecgm$sglucose), length.out=5),target)))+
ggplot2::theme_bw()+
ggplot2::theme(strip.background=element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))+
ggplot2::facet_grid( ~ week, scales="free", labeller = labeller(week=week.labs))+
ggplot2::annotate("text", x=range, y=6.95, label = "Target Range", color = "black", size =2, angle = 90, vjust=-0.3, fontface="italic")
ggplot2::ggsave(filename = sprintf('%sbyweek.png', i), plot = gi,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
}
## Obtain the "median" (50%) and other percentiles shown as if occurring in a single day, and plot as ambulatory glucose profile (AGP)
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
for(i in unique(aggregatecgm$studyid)){
quantiles <- aggregatecgm %>% filter(studyid == i) %>%
group_by(hourmin, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- quantiles %>% tidyr::spread(key = q, value = quantiles)
quantilesa <- quantiles %>% filter(cgmperiod == "a")
quantilesa$perc5 <- as.numeric(stats::smooth(quantilesa$q0.05,kind = "3R",twiceit = TRUE))
quantilesa$perc25 <- as.numeric(stats::smooth(quantilesa$q0.25,kind = "3R",twiceit = TRUE))
quantilesa$perc50 <- as.numeric(stats::smooth(quantilesa$q0.5,kind = "3R",twiceit = TRUE))
quantilesa$perc75 <- as.numeric(stats::smooth(quantilesa$q0.75,kind = "3R",twiceit = TRUE))
quantilesa$perc95 <- as.numeric(stats::smooth(quantilesa$q0.95,kind = "3R",twiceit = TRUE))
quantilesb <- quantiles %>% filter(cgmperiod == "b")
quantilesb$perc5 <- as.numeric(stats::smooth(quantilesb$q0.05,kind = "3R",twiceit = TRUE))
quantilesb$perc25 <- as.numeric(stats::smooth(quantilesb$q0.25,kind = "3R",twiceit = TRUE))
quantilesb$perc50 <- as.numeric(stats::smooth(quantilesb$q0.5,kind = "3R",twiceit = TRUE))
quantilesb$perc75 <- as.numeric(stats::smooth(quantilesb$q0.75,kind = "3R",twiceit = TRUE))
quantilesb$perc95 <- as.numeric(stats::smooth(quantilesb$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantilesa, quantilesb)
q <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"), linetype = 2, alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"), linetype = 3, alpha = 0.5)+
scale_colour_manual(values=c("dodgerblue","dodgerblue4","black"))+
geom_line(aes(y=perc50, color = "Median"), colour = "Black", show.legend = TRUE)+ geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
theme_bw()+
ggplot2::theme(legend.title = element_blank(), strip.background=element_rect(fill="white"))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = as.character(i))+
ggplot2::facet_grid(rows = vars(cgmperiod), labeller = labeller(cgmperiod=cgmperiod.labs))
ggplot2::ggsave(filename = sprintf('%sAGP.png', i), plot = q,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
}
## AGP for all patients, stratified by CGM period and DM status
aggregatecgm0 <- aggregatecgm %>% group_by(hourmin, cgmperiod, post_tx_dm) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a" & post_tx_dm == "0")
quantiles0b <- quantiles %>% filter(cgmperiod == "b" & post_tx_dm == "0")
quantiles1a <- quantiles %>% filter(cgmperiod == "a" & post_tx_dm == "1")
quantiles1b <- quantiles %>% filter(cgmperiod == "b" & post_tx_dm == "1")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
##############
##plot and facet by study_arm and cgmperiod
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
post_tx_dm.labs <- c("Non Diabetic", "Diabetic")
names(post_tx_dm.labs) <- c("0", "1")
k <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"),linetype = 2,alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"), linetype = 3, alpha = 0.5)+
ggplot2::scale_colour_manual(values=c("dodgerblue","dodgerblue4","black"))+
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = "Median"), colour = "Blue", show.legend = TRUE)+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15))+
ggplot2::theme(legend.title = ggplot2::element_blank(), strip.background=ggplot2::element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "All Patients")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
ggplot2::facet_grid(rows = vars(post_tx_dm), cols=vars(cgmperiod), labeller = labeller(cgmperiod=cgmperiod.labs, post_tx_dm=post_tx_dm.labs))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "all patients"), plot = k,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for non diabetic patients, stratified by study arm and cgm period
aggregatecgm0 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "0")
aggregatecgm0 <- aggregatecgm0 %>% group_by(hourmin, study_arm, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a" & study_arm == "0")
quantiles0b <- quantiles %>% filter(cgmperiod == "b" & study_arm == "0")
quantiles1a <- quantiles %>% filter(cgmperiod == "a" & study_arm == "1")
quantiles1b <- quantiles %>% filter(cgmperiod == "b" & study_arm == "1")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
##############
##plot and facet by study_arm and cgmperiod
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
study_arm.labs <- c("Standard Care", "Inulin")
names(study_arm.labs) <- c("0", "1")
h <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"),linetype = 2,alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"),linetype = 3, alpha = 0.5)+
ggplot2::scale_colour_manual(values=c("dodgerblue","dodgerblue4","black"))+
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = "Median"), colour = "Blue", show.legend = TRUE)+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15))+
ggplot2::theme(legend.title = ggplot2::element_blank(), strip.background=ggplot2::element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Non-diabetics")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
ggplot2::facet_grid(rows = vars(study_arm), cols=vars(cgmperiod), labeller = labeller(cgmperiod=cgmperiod.labs, study_arm=study_arm.labs))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "non-diabetic by study arm"), plot = h,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for non diabetic patients, and cgm period only
aggregatecgm0 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "0")
aggregatecgm0 <- aggregatecgm0 %>% group_by(hourmin, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a")
quantiles0b <- quantiles %>% filter(cgmperiod == "b")
quantiles1a <- quantiles %>% filter(cgmperiod == "a")
quantiles1b <- quantiles %>% filter(cgmperiod == "b")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
study_arm.labs <- c("Standard Care", "Inulin")
names(study_arm.labs) <- c("0", "1")
hh <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"),linetype = 2,alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"),linetype = 3, alpha = 0.5)+
ggplot2::scale_colour_manual(values=c("dodgerblue","dodgerblue4","black"))+
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = "Median"), colour = "Blue", show.legend = TRUE)+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15))+
ggplot2::theme(legend.title = ggplot2::element_blank(), strip.background=ggplot2::element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Non-diabetic")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
ggplot2::facet_grid(rows=vars(cgmperiod), labeller = labeller(cgmperiod=cgmperiod.labs, study_arm=study_arm.labs))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "non-diabetic"), plot = hh,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for DIABETIC patients, stratified by study arm and cgm period
aggregatecgm1 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "1")
aggregatecgm1 <- aggregatecgm1 %>% group_by(hourmin, study_arm, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm1 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a" & study_arm == "0")
quantiles0b <- quantiles %>% filter(cgmperiod == "b" & study_arm == "0")
quantiles1a <- quantiles %>% filter(cgmperiod == "a" & study_arm == "1")
quantiles1b <- quantiles %>% filter(cgmperiod == "b" & study_arm == "1")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
##plot and facet by study_arm and cgmperiod
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
study_arm.labs <- c("Standard Care", "Inulin")
names(study_arm.labs) <- c("0", "1")
j <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"),linetype = 2,alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"), linetype = 3, alpha = 0.5)+
ggplot2::geom_line(ggplot2::aes(y=perc50, color = perc50), colour = "blue", show.legend = TRUE)+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_y_continuous(breaks=c(0,3.9,7.5,10,15,20))+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::theme(legend.title = ggplot2::element_blank(), strip.background=ggplot2::element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size = 8),
axis.text.y = ggplot2::element_text(size = 8),legend.position = "right")+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Diabetics")+
ggplot2::facet_grid(rows = vars(study_arm), cols=vars(cgmperiod),
labeller = labeller(cgmperiod=cgmperiod.labs, study_arm=study_arm.labs))+
theme(panel.spacing.x = unit(-0.015, "lines"))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "diabetic by study arm"), plot = j,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for DIABETIC patients, stratify by cgm period
aggregatecgm0 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "1")
aggregatecgm0 <- aggregatecgm0 %>% group_by(hourmin, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a")
quantiles0b <- quantiles %>% filter(cgmperiod == "b")
quantiles1a <- quantiles %>% filter(cgmperiod == "a")
quantiles1b <- quantiles %>% filter(cgmperiod == "b")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
cgmperiod.labs <- c("Week 3-4", "Week 7-8")
names(cgmperiod.labs) <- c("a", "b")
study_arm.labs <- c("Standard Care", "Inulin")
names(study_arm.labs) <- c("0", "1")
jj <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50))+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"),linetype = 2,alpha = 0.5)+
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"),linetype = 3, alpha = 0.5)+
ggplot2::scale_colour_manual(values=c("dodgerblue","dodgerblue4","black"))+
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = "Median"), colour = "Blue", show.legend = TRUE)+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15))+
ggplot2::theme(legend.title = ggplot2::element_blank(), strip.background=ggplot2::element_rect(fill="white"),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8))+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Diabetic")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
ggplot2::facet_grid(rows=vars(cgmperiod), labeller = labeller(cgmperiod=cgmperiod.labs, study_arm=study_arm.labs))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "diabetic"), plot = jj,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for non diabetic patients, and cgm period only
aggregatecgm0 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "0")
aggregatecgm0 <- aggregatecgm0 %>% group_by(hourmin, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a")
quantiles0b <- quantiles %>% filter(cgmperiod == "b")
quantiles1a <- quantiles %>% filter(cgmperiod == "a")
quantiles1b <- quantiles %>% filter(cgmperiod == "b")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
hh <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50, color = cgmperiod)) +
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"), linetype = 2, alpha = 0.2) +
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"), linetype = 3, alpha = 0.4) +
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = cgmperiod), show.legend = TRUE)+
ggplot2::scale_color_brewer(palette = "Set1", labels = c("Weeks 3-4", "Weeks 7-8"))+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15))+
ggplot2::theme(legend.title = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8), legend.position = "top")+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Non-diabetic Patients")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
guides(color=guide_legend(override.aes=list(fill=NA)))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "non-diabetic overlay"), plot = hh,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
##plot all aggregate results on the one graph, for diabetic patients, and cgm period only
aggregatecgm0 <- aggregatecgm %>% dplyr::filter(post_tx_dm == "1")
aggregatecgm0 <- aggregatecgm0 %>% group_by(hourmin, cgmperiod) %>%
summarise(quantiles = quantile(sglucose, c(0.05, 0.25, 0.5, 0.75, 0.95)), q = c("q0.05", "q0.25", "q0.5", "q0.75", "q0.95"))
quantiles <- aggregatecgm0 %>% tidyr::spread(key = q, value = quantiles)
quantiles0a <- quantiles %>% filter(cgmperiod == "a")
quantiles0b <- quantiles %>% filter(cgmperiod == "b")
quantiles1a <- quantiles %>% filter(cgmperiod == "a")
quantiles1b <- quantiles %>% filter(cgmperiod == "b")
quantiles0a$perc5 <- as.numeric(stats::smooth(quantiles0a$q0.05,kind = "3R",twiceit = TRUE))
quantiles0a$perc25 <- as.numeric(stats::smooth(quantiles0a$q0.25,kind = "3R",twiceit = TRUE))
quantiles0a$perc50 <- as.numeric(stats::smooth(quantiles0a$q0.5,kind = "3R",twiceit = TRUE))
quantiles0a$perc75 <- as.numeric(stats::smooth(quantiles0a$q0.75,kind = "3R",twiceit = TRUE))
quantiles0a$perc95 <- as.numeric(stats::smooth(quantiles0a$q0.95,kind = "3R",twiceit = TRUE))
quantiles0b$perc5 <- as.numeric(stats::smooth(quantiles0b$q0.05,kind = "3R",twiceit = TRUE))
quantiles0b$perc25 <- as.numeric(stats::smooth(quantiles0b$q0.25,kind = "3R",twiceit = TRUE))
quantiles0b$perc50 <- as.numeric(stats::smooth(quantiles0b$q0.5,kind = "3R",twiceit = TRUE))
quantiles0b$perc75 <- as.numeric(stats::smooth(quantiles0b$q0.75,kind = "3R",twiceit = TRUE))
quantiles0b$perc95 <- as.numeric(stats::smooth(quantiles0b$q0.95,kind = "3R",twiceit = TRUE))
quantiles1a$perc5 <- as.numeric(stats::smooth(quantiles1a$q0.05,kind = "3R",twiceit = TRUE))
quantiles1a$perc25 <- as.numeric(stats::smooth(quantiles1a$q0.25,kind = "3R",twiceit = TRUE))
quantiles1a$perc50 <- as.numeric(stats::smooth(quantiles1a$q0.5,kind = "3R",twiceit = TRUE))
quantiles1a$perc75 <- as.numeric(stats::smooth(quantiles1a$q0.75,kind = "3R",twiceit = TRUE))
quantiles1a$perc95 <- as.numeric(stats::smooth(quantiles1a$q0.95,kind = "3R",twiceit = TRUE))
quantiles1b$perc5 <- as.numeric(stats::smooth(quantiles1b$q0.05,kind = "3R",twiceit = TRUE))
quantiles1b$perc25 <- as.numeric(stats::smooth(quantiles1b$q0.25,kind = "3R",twiceit = TRUE))
quantiles1b$perc50 <- as.numeric(stats::smooth(quantiles1b$q0.5,kind = "3R",twiceit = TRUE))
quantiles1b$perc75 <- as.numeric(stats::smooth(quantiles1b$q0.75,kind = "3R",twiceit = TRUE))
quantiles1b$perc95 <- as.numeric(stats::smooth(quantiles1b$q0.95,kind = "3R",twiceit = TRUE))
quantiles <- rbind(quantiles0a, quantiles0b, quantiles1a, quantiles1b)
kk <- ggplot2::ggplot(data = quantiles, ggplot2::aes(x = hourmin, y=perc50, color = cgmperiod)) +
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc5,ymax = quantiles$perc95, fill = "5th to 95th Percentile"), linetype = 2, alpha = 0.2) +
ggplot2::geom_ribbon(ggplot2::aes(ymin = quantiles$perc25,ymax = quantiles$perc75, fill = "Interquartile Range"), linetype = 3, alpha = 0.4) +
ggplot2::geom_line(data=quantiles,ggplot2::aes(y=perc50, color = cgmperiod), show.legend = TRUE)+
ggplot2::scale_color_brewer(palette = "Set1", labels = c("Weeks 3-4", "Weeks 7-8"))+
ggplot2::geom_hline(yintercept = c(3.9,10), linetype="solid", colour = "red")+
ggplot2::scale_x_datetime(labels = function(x) format(x, format = "%H:%M"), date_breaks = "3 hours", limits = lims, expand=c(0,0))+
ggplot2::theme_bw()+
ggplot2::scale_y_continuous(breaks=c(0,3.9,5,7.5,10,12.5,15,20,25))+
ggplot2::theme(legend.title = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size =8),
axis.text.y = ggplot2::element_text(size = 8), legend.position = "top")+
ggplot2::ylab("Sensor Glucose (mmol/L)")+
ggplot2::xlab("Time (hour)")+
ggplot2::labs(title = "Ambulatory Glucose Profile", subtitle = "Diabetic Patients")+
theme(panel.spacing.x = unit(-0.015, "lines"))+
guides(color=guide_legend(override.aes=list(fill=NA)))
ggplot2::ggsave(filename = sprintf('%sAGP.png', "diabetic overlay"), plot = kk,
path = output,
dpi = 300, width = 17, height = 10, units = "cm")
}
graphcgm("Practice","Graphs","metadata")