Code
# estimated_Theta=readRDS("~/estimated_theta_all38.rds")
# adjusted_gp_mean=readRDS("~/adjusted_gp_mean_all38.rds")
# gp_mean_array=readRDS("~/gp_mean_array_all38.rds")
# gp_means_pop=readRDS("~/gp_means_pop_all38.rds")
library(ggplot2)
library(data.table)
library(ggsci)
library(dplyr)
library(ATM)
beta=ATM::UKB_HES_10topics # age times disease times topics
data=ATM::HES_age_example
data$round_age=round(data$age_diag,0)
# Prepare the data by grouping and summarizing
data_grouped <- data %>%
group_by(eid, round_age) %>%
summarise(diagnoses = list(diag_icd10), .groups = 'drop')%>%ungroup()
D=length(unique(data_grouped$eid)) # To test individuals
#D=10
K <- dim(beta)[3] # Number of topics
T <- dim(beta)[1] # Number of time points
csv=fread("~/Library/CloudStorage/Dropbox-Personal/41588_2023_1522_MOESM4_ESM.csv")
topics=unique((csv$V1))[4:13]
# estimated_Theta=readRDS("estimated_theta_all_log_38.rds")
# matplot(t(apply(estimated_Theta[,,c(1:3)],c(2,3),mean)),type = "l")
# adjusted_gp_mean=readRDS("adjusted_gp_mean_all_log_38.rds")
# gp_mean_array=readRDS("gp_mean_array_all_log_38.rds")
# gp_means_pop=readRDS("gp_means_pop_all_log_38.rds")
estimated_Theta=readRDS("estimated_theta_all_log_10_simk.rds")
matplot(t(apply(estimated_Theta[,,c(1:3)],c(2,3),mean)),type = "l")
Code
adjusted_gp_mean=readRDS("adjusted_gp_mean_all_log_10_simk.rds")
gp_mean_array=readRDS("gp_mean_array_all_log_10_simk.rds")
gp_means_pop=readRDS("gp_means_pop_all_log_10_simk.rds")
pt_ids=unique(data$eid)[1:dim(estimated_Theta)[1]]
data_grouped=data_grouped[data_grouped$eid%in%pt_ids,]
dimnames(estimated_Theta)=dimnames(adjusted_gp_mean)=dimnames(gp_mean_array)=list(pt_ids,topics,c(1:81))
# Assuming 'estimated_Theta', 'adjusted_gp_mean', and 'gp_means_pop' are loaded into your R session
# Set the dimensions for plotting
num_individuals <- dim(estimated_Theta)[1]
num_topics <- dim(estimated_Theta)[2]
num_time_points <- dim(estimated_Theta)[3]
# Sample a random individual
population_theta <- gp_means_pop[,-c(1:3)]
# Create a data frame for plotting
time <- 4:num_time_points
df_population <- data.frame(time = rep(time, num_topics),
topic = rep(topics, each = num_time_points-3),
theta = as.vector(t(population_theta)))
# Plot for the individual
ggplot(df_population, aes(x = time, y = theta, color = topic)) +
geom_line() +
labs(title = sprintf("Topic Proportions Over Time for Population"),
x = "Time Point",
y = "Population GP Mean",
color = "Topic") +scale_color_d3(
palette = c("category20"),alpha = 1)+
theme_minimal() 
Code
dg=data_grouped%>%group_by(eid)%>%summarise(n=length(eid))%>%arrange(desc(n))
for(i in 1:10){
sample_id <- as.character(dg$eid[i])
# Extract data for the individual and population
individual_theta <- estimated_Theta[sample_id, ,-c(1:3) ]
individual_gp_means <- adjusted_gp_mean[sample_id, ,-c(1:3) ]
df_individual <- data.frame(time = rep(time, num_topics),
topic = rep(topics, each = num_time_points-3),
theta = as.vector(t(individual_gp_means)))
# Plot for the individual
library(ggsci)
print(ggplot(df_individual, aes(x = time, y = theta, color = topic)) +
geom_line() +
labs(title = paste("Topic Proportions Over Time for Individual", sample_id),
x = "Time Point",
y = "Adjusted GP Mean",
color = "Topic") +scale_color_d3(
palette = c("category20"),alpha = 1)+
theme_minimal())
#data.frame(data_grouped[data_grouped$eid%in%sample_id,])
disease_merge=merge(data,ATM::disease_info_phecode_icd10,by.x="diag_icd10",by.y="phecode")
d=disease_merge[disease_merge$eid%in%sample_id,]%>%arrange(round_age)
print(d[,c("round_age","phenotype","exclude_name")])
#nw <- loading2weights(HES_age_example, ds_list = UKB_349_disease, topics = UKB_HES_10topics)
#saveRDS(nw,"~/Library/CloudStorage/Dropbox-Personal/ATM_simweights.rds")
nw=readRDS("~/Library/CloudStorage/Dropbox-Personal/ATM_simweights.rds")
new_weights=nw$topic_weights
tw=data.frame(new_weights[new_weights$eid%in%sample_id,])
names(tw)[2:11]=topics
mt=melt(tw,id.vars="eid")
gp=ggplot(mt,aes(as.factor(eid),value,fill=variable))+geom_bar(stat="identity")+
labs(y="Topic Weight",x="Pt ID",fill="Inferred Topic")+scale_fill_d3(
palette = c("category20"),alpha = 1)
print(gp)
}
round_age phenotype
1 42 Thyrotoxicosis with or without goiter
2 42 Hypothyroidism NOS
3 42 Type 1 diabetes
4 43 Type 2 diabetes
5 46 Reflux esophagitis
6 47 Hemiplegia
7 47 Rheumatism, unspecified and fibrositis
8 48 Osteoarthrosis, generalized
9 49 Chronic sinusitis
10 50 Essential hypertension
11 51 Other chronic ischemic heart disease, unspecified
12 51 Lump or mass in breast
13 52 Pulmonary heart disease
14 53 Migraine
15 54 Inflammatory and toxic neuropathy
16 54 Retinal vascular changes and abnomalities
17 54 Coronary atherosclerosis
18 55 Cerebral ischemia
19 56 Phlebitis and thrombophlebitis of lower extremities
20 57 Myalgia and myositis unspecified
21 58 Hemorrhage of gastrointestinal tract
22 59 Disorders of calcium/phosphorus metabolism
exclude_name
1 endocrine/metabolic
2 endocrine/metabolic
3 endocrine/metabolic
4 endocrine/metabolic
5 digestive
6 neurological
7 musculoskeletal
8 musculoskeletal
9 respiratory
10 circulatory system
11 circulatory system
12 genitourinary
13 circulatory system
14 neurological
15 neurological
16 sense organs
17 circulatory system
18 circulatory system
19 circulatory system
20 symptoms
21 digestive
22 endocrine/metabolic
round_age phenotype
1 44 Chronic periodontitis
2 45 Hypotension NOS
3 45 Lump or mass in breast
4 48 Esophagitis, GERD and related diseases
5 49 Bipolar
6 49 Irritable Bowel Syndrome
7 50 Rheumatism, unspecified and fibrositis
8 51 Other disorders of intestine
9 52 Urinary tract infection
10 54 Hypothyroidism NOS
11 55 Other chronic ischemic heart disease, unspecified
12 55 Cellulitis and abscess of arm/hand
13 56 Iron deficiency anemias, unspecified or not due to blood loss
14 56 Umbilical hernia
15 56 Chronic ulcer of skin
16 56 Other acquired deformities of limbs
17 58 Chronic airway obstruction
18 58 Thoracic or lumbosacral neuritis or radiculitis, unspecified
19 59 Asthma
20 59 Other and unspecified disc disorder
21 60 Enthesopathy
22 60 Osteoporosis NOS
23 61 Arthropathy NOS
exclude_name
1 digestive
2 circulatory system
3 genitourinary
4 digestive
5 mental disorders
6 digestive
7 musculoskeletal
8 digestive
9 genitourinary
10 endocrine/metabolic
11 circulatory system
12 dermatologic
13 hematopoietic
14 digestive
15 dermatologic
16 musculoskeletal
17 respiratory
18 symptoms
19 respiratory
20 musculoskeletal
21 musculoskeletal
22 musculoskeletal
23 musculoskeletal
round_age phenotype
1 49 Unstable angina (intermediate coronary syndrome)
2 50 Cerebral artery occlusion, with cerebral infarction
3 50 Calculus of ureter
4 51 Iron deficiency anemias, unspecified or not due to blood loss
5 52 Pyelonephritis
6 52 Calculus of kidney
7 53 Other hypertrophic and atrophic conditions of skin
8 54 Essential hypertension
9 56 Late effects of cerebrovascular disease
10 56 Diaphragmatic hernia
11 56 Blood in stool
12 57 Respiratory failure
13 58 Chronic airway obstruction
14 58 Cholecystitis without cholelithiasis
15 59 Other chronic nonalcoholic liver disease
16 59 Cholelithiasis
17 60 Visual disturbances
18 60 Asthma
19 60 Diverticulosis
20 60 Cholelithiasis with other cholecystitis
21 65 Pneumococcal pneumonia
22 66 Streptococcus infection
23 66 Hypoglycemia
24 66 Cerebrovascular disease
25 66 Functional disorders of bladder
26 66 Pain in joint
exclude_name
1 circulatory system
2 circulatory system
3 genitourinary
4 hematopoietic
5 genitourinary
6 genitourinary
7 dermatologic
8 circulatory system
9 circulatory system
10 digestive
11 digestive
12 respiratory
13 respiratory
14 digestive
15 digestive
16 digestive
17 sense organs
18 respiratory
19 digestive
20 digestive
21 respiratory
22 infectious diseases
23 endocrine/metabolic
24 circulatory system
25 genitourinary
26 musculoskeletal
round_age phenotype
1 33 Back pain
2 34 Noninfectious gastroenteritis
3 36 Acquired spondylolisthesis
4 37 Irritable Bowel Syndrome
5 37 Neuralgia, neuritis, and radiculitis NOS
6 38 GERD
7 38 Arthropathy NOS
8 40 Essential hypertension
9 41 Staphylococcus infections
10 41 E. coli
11 41 Angina pectoris
12 41 Hypotension NOS
13 42 Bacterial infection NOS
14 45 Noninflammatory disorders of vagina
15 45 Disorder of skin and subcutaneous tissue NOS
16 46 Ulcer of esophagus
17 47 Gastritis and duodenitis
18 48 Decubitus ulcer
19 50 Pulmonary collapse; interstitial and compensatory emphysema
20 50 Constipation
exclude_name
1 symptoms
2 digestive
3 musculoskeletal
4 digestive
5 symptoms
6 digestive
7 musculoskeletal
8 circulatory system
9 infectious diseases
10 infectious diseases
11 circulatory system
12 circulatory system
13 infectious diseases
14 genitourinary
15 dermatologic
16 digestive
17 digestive
18 dermatologic
19 respiratory
20 digestive
round_age phenotype
1 54 Hypothyroidism NOS
2 54 Essential hypertension
3 54 Hemorrhage of rectum and anus
4 55 Obesity
5 55 Ventral hernia
6 57 Type 2 diabetes
7 57 Coronary atherosclerosis
8 58 Polymyalgia Rheumatica
9 59 Senile cataract
10 59 Orthostatic hypotension
11 59 Urinary incontinence
12 60 Rheumatoid arthritis
13 61 Diabetic retinopathy
14 61 Hemorrhoids
15 61 Other disorders of gallbladder
16 61 Hematemesis
17 61 Congenital anomalies of great vessels
18 62 Staphylococcus infections
19 62 Type 2 diabetes with ophthalmic manifestations
20 62 Hypoglycemia
21 62 Hypotension NOS
22 62 Pneumococcal pneumonia
23 62 Noninfectious gastroenteritis
24 62 Urinary tract infection
25 63 Lipoma of skin and subcutaneous tissue
26 63 Chronic ulcer of skin
27 65 Phlebitis and thrombophlebitis of lower extremities
28 67 Aortic valve disease
29 68 Atrial fibrillation and flutter
30 68 Chronic renal failure [CKD]
exclude_name
1 endocrine/metabolic
2 circulatory system
3 digestive
4 endocrine/metabolic
5 digestive
6 endocrine/metabolic
7 circulatory system
8 musculoskeletal
9 sense organs
10 circulatory system
11 genitourinary
12 musculoskeletal
13 endocrine/metabolic
14 circulatory system
15 digestive
16 digestive
17 congenital anomalies
18 infectious diseases
19 endocrine/metabolic
20 endocrine/metabolic
21 circulatory system
22 respiratory
23 digestive
24 genitourinary
25 neoplasms
26 dermatologic
27 circulatory system
28 circulatory system
29 circulatory system
30 genitourinary
round_age phenotype
1 31 Chronic tonsillitis and adenoiditis
2 31 Other upper respiratory disease
3 32 Atrial fibrillation and flutter
4 32 Heart failure NOS
5 32 Cholecystitis without cholelithiasis
6 32 Myalgia and myositis unspecified
7 33 Bacterial infection NOS
8 33 Staphylococcus infections
9 34 Hypercholesterolemia
10 35 Reflux esophagitis
11 36 Hyperlipidemia
12 40 Other local infections of skin and subcutaneous tissue
13 43 Hypertensive chronic kidney disease
14 43 GERD
15 44 Type 2 diabetes
16 45 Obesity
17 46 Constipation
18 48 Osteoarthritis; localized
exclude_name
1 respiratory
2 respiratory
3 circulatory system
4 circulatory system
5 digestive
6 symptoms
7 infectious diseases
8 infectious diseases
9 endocrine/metabolic
10 digestive
11 endocrine/metabolic
12 dermatologic
13 circulatory system
14 digestive
15 endocrine/metabolic
16 endocrine/metabolic
17 digestive
18 musculoskeletal
round_age phenotype
1 38 Other disorders of the kidney and ureters
2 39 Ingrowing nail
3 44 Back pain
4 46 Essential hypertension
5 46 Osteoarthrosis, localized, primary
6 47 Other disorders of bone and cartilage
7 50 Staphylococcus infections
8 50 Other hypertrophic and atrophic conditions of skin
9 52 Benign neoplasm of skin
10 52 Ventral hernia
11 52 Urinary tract infection
12 54 Scar conditions and fibrosis of skin
13 55 Hematemesis
14 56 Myocardial infarction
15 57 Thyrotoxicosis with or without goiter
16 57 Hemorrhoids
17 58 Transient cerebral ischemia
exclude_name
1 genitourinary
2 dermatologic
3 symptoms
4 circulatory system
5 musculoskeletal
6 musculoskeletal
7 infectious diseases
8 dermatologic
9 neoplasms
10 digestive
11 genitourinary
12 dermatologic
13 digestive
14 circulatory system
15 endocrine/metabolic
16 circulatory system
17 circulatory system
round_age phenotype exclude_name
1 37 Prolapse of vaginal walls genitourinary
2 38 Other disorders of bladder genitourinary
3 39 Benign neoplasm of colon neoplasms
4 40 Obesity endocrine/metabolic
5 40 Anal and rectal conditions digestive
6 41 Endometriosis genitourinary
7 45 Candidiasis infectious diseases
8 45 Duodenitis digestive
9 48 Other disorders of soft tissues musculoskeletal
10 49 Gastritis and duodenitis digestive
11 49 Functional disorders of bladder genitourinary
12 49 Pain in limb symptoms
13 50 Ventral hernia digestive
14 50 Other intestinal obstruction digestive
15 52 Hypercholesterolemia endocrine/metabolic
16 53 Chronic ulcer of skin dermatologic
17 54 Tobacco use disorder mental disorders
round_age phenotype exclude_name
1 59 Bladder neck obstruction genitourinary
2 62 Arthropathy NOS musculoskeletal
3 62 Internal derangement of knee injuries & poisonings
4 63 Type 2 diabetes endocrine/metabolic
5 64 Hypercholesterolemia endocrine/metabolic
6 65 Spinal stenosis musculoskeletal
7 65 Osteoarthritis; localized musculoskeletal
8 66 Angina pectoris circulatory system
9 66 Peripheral vascular disease, unspecified circulatory system
10 66 Urinary tract infection genitourinary
11 66 Hyperplasia of prostate genitourinary
12 68 Osteoarthrosis, generalized musculoskeletal
13 69 Sleep apnea neurological
14 69 Chronic airway obstruction respiratory
15 70 Bacterial infection NOS infectious diseases
16 70 Pleurisy; pleural effusion respiratory
17 70 Cyst of kidney, acquired genitourinary
18 71 Other disorders of bladder genitourinary
19 72 Late effects of cerebrovascular disease circulatory system
20 73 Myocardial infarction circulatory system
21 73 Congestive heart failure (CHF) NOS circulatory system
round_age phenotype
1 60 Type 1 diabetes
2 60 Unstable angina (intermediate coronary syndrome)
3 60 Other chronic ischemic heart disease, unspecified
4 61 Strabismus (not specified as paralytic)
5 62 Benign neoplasm of ovary
6 64 Hypothyroidism NOS
7 64 Other upper respiratory disease
8 64 Other diseases of respiratory system, NEC
9 65 Occlusion of cerebral arteries
10 66 Benign neoplasm of other parts of digestive system
11 66 Type 2 diabetes with ophthalmic manifestations
12 66 Myocardial infarction
13 66 Cerebral ischemia
14 67 Congestive heart failure (CHF) NOS
15 67 Gastric ulcer
16 67 Gastritis and duodenitis
17 67 Acute gastritis
18 67 Anal and rectal polyp
19 68 Hypertensive chronic kidney disease
20 69 Cardiomegaly
21 70 Hyperlipidemia
22 71 Rheumatism, unspecified and fibrositis
23 71 Osteoporosis NOS
24 73 Other retinal disorders
exclude_name
1 endocrine/metabolic
2 circulatory system
3 circulatory system
4 sense organs
5 neoplasms
6 endocrine/metabolic
7 respiratory
8 respiratory
9 circulatory system
10 neoplasms
11 endocrine/metabolic
12 circulatory system
13 circulatory system
14 circulatory system
15 digestive
16 digestive
17 digestive
18 digestive
19 circulatory system
20 circulatory system
21 endocrine/metabolic
22 musculoskeletal
23 musculoskeletal
24 sense organs