From a335ace1ee6af4bcfcd607bd4808bfad705d39b0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 1 Jan 2020 21:34:41 -0600
Subject: [PATCH] Get repository working
---
config.toml | 12 +-
data/repository/filters.json | 66 +
data/repository/repository.json | 10152 +++++++++++++++++++++
data/scRNAseq_huPr_D/updated_cleaned.csv | 292 -
layouts/custom/contact.html | 8 +-
layouts/custom/hu.donor.deep.html | 18 +-
layouts/custom/hu.donor.shallow.html | 318 +-
layouts/custom/people.html | 4 +
layouts/custom/publications.html | 53 +-
layouts/custom/repository.html | 1073 ++-
layouts/custom/research.html | 116 +-
layouts/custom/sc.data.html | 8 +-
12 files changed, 11429 insertions(+), 691 deletions(-)
create mode 100644 data/repository/filters.json
create mode 100644 data/repository/repository.json
delete mode 100644 data/scRNAseq_huPr_D/updated_cleaned.csv
diff --git a/config.toml b/config.toml
index 22ac651..4acf35b 100644
--- a/config.toml
+++ b/config.toml
@@ -49,12 +49,12 @@ paginate = 10
weight = 3
identifier = "publications"
url = "/publications/"
-# [[menu.main]]
-# name = "Biorepository"
-# pre = "<i class='fas fa-stethoscope fa-fw'></i>"
-# weight = 4
-# identifier = "repository"
-# url = "/repository/"
+ [[menu.main]]
+ name = "Biorepository"
+ pre = "<i class='fas fa-stethoscope fa-fw'></i>"
+ weight = 4
+ identifier = "repository"
+ url = "/repository/"
[[menu.main]]
name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>"
diff --git a/data/repository/filters.json b/data/repository/filters.json
new file mode 100644
index 0000000..633c958
--- /dev/null
+++ b/data/repository/filters.json
@@ -0,0 +1,66 @@
+[
+ {"id": "disease", "parent": "#", "text": "Disease Phenotype", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
+ {"id": "disease.b", "parent":"disease", "text": "BPH"},
+ {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
+ {"id": "demographics", "parent": "#", "text": "Demographics", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
+ {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
+ {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
+ {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
+ {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
+ {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "age.40", "parent":"age", "text": "<40yo"},
+ {"id": "age.50", "parent":"age", "text": "41-50yo"},
+ {"id": "age.60", "parent":"age", "text": "51-60yo"},
+ {"id": "age.70", "parent":"age", "text": "61-70yo"},
+ {"id": "age.80", "parent":"age", "text": "71-80yo"},
+ {"id": "age.90", "parent":"age", "text": "81-90yo"},
+ {"id": "age.100", "parent":"age", "text": "91+yo"},
+ {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
+ {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
+ {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
+ {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
+ {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
+ {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
+ {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
+ {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
+ {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
+ {"id": "t2d.n", "parent":"t2d", "text": "No"},
+ {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
+ {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
+ {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
+ {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
+ {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
+ {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
+ {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
+ {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
+ {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
+ {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
+ {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
+ {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
+ {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
+ {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
+ {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
+ {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
+ {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
+ {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
+ {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
+ {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
+ {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
+ {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
+ {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
+ {"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
+ {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+]
\ No newline at end of file
diff --git a/data/repository/repository.json b/data/repository/repository.json
new file mode 100644
index 0000000..d030e11
--- /dev/null
+++ b/data/repository/repository.json
@@ -0,0 +1,10152 @@
+[
+ {
+ "PatientID": "dws000001",
+ "Study ID": 1,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 62,
+ "Ethnicity": "Cauc",
+ "AUASS": 21,
+ "Peak flowrate": 6.1,
+ "Post void residual": 157,
+ "Prostate volume": 100,
+ "PSA": 9.62,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": 60,
+ "BMI": 29.1,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 286,
+ "HBA1c": 7.2,
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000002",
+ "Study ID": 2,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 65,
+ "Ethnicity": "Hisp",
+ "AUASS": "unknown",
+ "Peak flowrate": 4.1,
+ "Post void residual": 76,
+ "Prostate volume": 200,
+ "PSA": 10.9,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": 48,
+ "BMI": 29.9,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 164,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000003",
+ "Study ID": 3,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 70,
+ "Ethnicity": "Cauc",
+ "AUASS": 8,
+ "Peak flowrate": 4.1,
+ "Post void residual": 170,
+ "Prostate volume": 208.9,
+ "PSA": 2,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 32.7,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000004",
+ "Study ID": 4,
+ "Disease Status": "BPH",
+ "BPH surgery": "TURP",
+ "Age": 61,
+ "Ethnicity": "Cauc",
+ "AUASS": 13,
+ "Peak flowrate": 7.7,
+ "Post void residual": 200,
+ "Prostate volume": 33,
+ "PSA": 1,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.2,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000005",
+ "Study ID": 5,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 83,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": "unknown",
+ "Post void residual": 457,
+ "Prostate volume": 138,
+ "PSA": 4.36,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 27.2,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 112,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000006",
+ "Study ID": 6,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 61,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 10.2,
+ "Post void residual": 620,
+ "Prostate volume": 117,
+ "PSA": 3.6,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.5,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 144,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000007",
+ "Study ID": 7,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 54,
+ "Ethnicity": "Hisp",
+ "AUASS": 17,
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 111.7,
+ "PSA": 14.2,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.3,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 224,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 0,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000008",
+ "Study ID": 8,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 80,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 3.1,
+ "Post void residual": 146,
+ "Prostate volume": 140,
+ "PSA": 6.7,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 27.8,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000009",
+ "Study ID": 9,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 73,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 10.3,
+ "Post void residual": 141,
+ "Prostate volume": 130,
+ "PSA": 8.92,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": 17,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.8,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 169,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000010",
+ "Study ID": 10,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 67,
+ "Ethnicity": "Cauc",
+ "AUASS": 26,
+ "Peak flowrate": 2.6,
+ "Post void residual": 323,
+ "Prostate volume": 160,
+ "PSA": 9.2,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 29.8,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 112,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000011",
+ "Study ID": 11,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 56,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": 3.3,
+ "Post void residual": 313,
+ "Prostate volume": 110,
+ "PSA": "unknown",
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 25.5,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 127,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000012",
+ "Study ID": 12,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 68,
+ "Ethnicity": "Cauc",
+ "AUASS": 31,
+ "Peak flowrate": 11.4,
+ "Post void residual": 545,
+ "Prostate volume": 150,
+ "PSA": 7.1,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.4,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 217,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000013",
+ "Study ID": 13,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 71,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 140,
+ "PSA": 3.2,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 30.3,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 121,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000014",
+ "Study ID": 14,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 60,
+ "Ethnicity": "AA",
+ "AUASS": 9,
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 106.4,
+ "PSA": 5.74,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 39.1,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 95,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000015",
+ "Study ID": 20,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 58,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": 12.3,
+ "Post void residual": 219,
+ "Prostate volume": 158,
+ "PSA": 21.33,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": 60,
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.4,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 133,
+ "HBA1c": 6.6,
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000016",
+ "Study ID": 24,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 67,
+ "Ethnicity": "Cauc",
+ "AUASS": 19,
+ "Peak flowrate": 3.8,
+ "Post void residual": 147,
+ "Prostate volume": 126,
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+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ }
+]
diff --git a/data/scRNAseq_huPr_D/updated_cleaned.csv b/data/scRNAseq_huPr_D/updated_cleaned.csv
deleted file mode 100644
index a9533ca..0000000
--- a/data/scRNAseq_huPr_D/updated_cleaned.csv
+++ /dev/null
@@ -1,292 +0,0 @@
-PatientID,Study ID,Disease Status,BPH surgery,Age,Ethnicity,AUASS,Peak flowrate,Post void residual,Prostate volume,PSA,Urinary retention,5ARI,5ARI length (months),Alpha blocker,Alpha blocker length (months),BMI,Type 2 diabetes,Blood glucose,HBA1c,Hyperlipidemia,Hypertension,Serum,Urine,Buffy coat,Cryopreserved single cells,Flash frozen,Paraffin block,OCT block,Matching bladder,Matching Seminal vesicle,Matching vas deferens,Matching ureter
-bph00001,1,BPH,Simple,62,Cauc,21,6.1,157,100,9.62,1,0,NULL,1,60,29.1,1,286,7.2,1,1,0,0,0,0,1,1,1,0,0,0,0
-bph00002,2,BPH,Simple,65,Hisp,NULL,4.1,76,200,10.9,1,0,NULL,1,48,29.9,0,164,NULL,1,1,0,0,0,0,1,1,1,0,0,0,0
-bph00003,3,BPH,Simple,70,Cauc,8,4.1,170,208.9,2,0,0,NULL,1,NULL,32.7,0,NULL,NULL,1,1,0,0,0,0,1,1,1,0,0,0,0
-bph00004,4,BPH,TURP,61,Cauc,13,7.7,200,33,1,0,1,NULL,1,NULL,28.2,0,NULL,NULL,1,0,0,0,0,0,1,1,1,0,0,0,0
-bph00005,5,BPH,Simple,83,Cauc,NULL,NULL,457,138,4.36,1,1,NULL,1,NULL,27.2,0,112,NULL,0,1,0,0,0,0,1,1,1,0,0,0,0
-bph00006,6,BPH,Simple,61,Cauc,17,10.2,620,117,3.6,0,1,NULL,0,NULL,31.5,0,144,NULL,1,0,0,0,0,1,1,1,1,0,0,0,0
-bph00007,7,BPH,Simple,54,Hisp,17,NULL,NULL,111.7,14.2,1,1,NULL,1,NULL,28.3,1,224,NULL,1,1,0,0,0,1,0,1,1,0,0,0,0
-bph00008,8,BPH,Simple,80,Cauc,17,3.1,146,140,6.7,1,1,NULL,1,NULL,27.8,0,NULL,NULL,1,0,0,0,0,1,1,1,1,0,0,0,0
-bph00009,9,BPH,Simple,73,Cauc,17,10.3,141,130,8.92,1,1,17,0,NULL,31.8,1,169,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00010,10,BPH,Simple,67,Cauc,26,2.6,323,160,9.2,0,0,NULL,1,NULL,29.8,0,112,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00011,11,BPH,Simple,56,Cauc,NULL,3.3,313,110,NULL,0,0,NULL,1,NULL,25.5,0,127,NULL,0,0,0,0,0,0,1,1,1,0,0,0,0
-bph00012,12,BPH,Simple,68,Cauc,31,11.4,545,150,7.1,1,0,NULL,0,NULL,31.4,1,217,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00013,13,BPH,Simple,71,Cauc,NULL,NULL,NULL,140,3.2,1,0,NULL,0,NULL,30.3,0,121,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00014,14,BPH,Simple,60,AA,9,NULL,NULL,106.4,5.74,0,0,NULL,0,NULL,39.1,0,95,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00015,20,BPH,Simple,58,Cauc,NULL,12.3,219,158,21.33,0,1,60,1,NULL,28.4,1,133,6.6,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00016,24,BPH,Simple,67,Cauc,19,3.8,147,126,4.85,0,1,24,1,NULL,26.2,0,NULL,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00017,54,BPH,Simple,74,Cauc,15,12.2,260,207,6,0,1,NULL,1,NULL,27.9,0,104,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00018,60,BPH,Simple,61,Cauc,NULL,NULL,NULL,254,7.5,1,0,NULL,1,NULL,30.8,0,107,NULL,1,1,0,0,0,0,1,1,1,0,0,0,0
-bph00019,61,BPH,Simple,68,Cauc,13,9.8,373,107,6.7,0,0,NULL,0,NULL,26.2,0,124,NULL,1,0,0,0,0,1,1,1,1,0,0,0,0
-bph00020,65,BPH,Simple,56,AA,22,NULL,NULL,200,6.7,0,1,discontinued,1,NULL,33.9,0,100,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00021,76,BPH,Simple,72,unknown,NULL,29.5,401,142,3.4,1,1,NULL,1,NULL,23,0,93,NULL,0,0,0,0,0,1,1,1,1,0,0,0,0
-bph00022,81,BPH,Simple,65,Cauc,NULL,13.6,50,100,13.3,0,0,NULL,1,12,34.8,0,117,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00023,85,BPH,Simple,74,Cauc,NULL,NULL,272,240,14.63,0,0,NULL,0,NULL,31.4,0,136,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00024,89,BPH,Simple,64,Cauc,15,5.2,165,139,5.1,0,0,NULL,1,NULL,29.3,0,116,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00025,90,BPH,Simple,50,Cauc,32,NULL,NULL,107.6,2.3,0,0,NULL,1,NULL,34.2,0,118,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00026,93,BPH,Simple,54,Hisp,NULL,13,127,120,3.64,0,1,NULL,0,NULL,30.5,1,143,6.6,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00027,95,BPH,Simple,71,Cauc,16,NULL,NULL,140,10,1,0,NULL,0,NULL,31.6,0,139,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00028,96,BPH,Simple,72,AA,14,NULL,164,164,9.79,0,1,discontinued,1,NULL,26.6,0,116,NULL,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00029,97,BPH,Simple,63,Hisp,NULL,NULL,NULL,121,11.8,0,1,NULL,1,NULL,27.1,1,330,10.2,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00030,98,BPH,TURP,69,AA,NULL,14,55,32,0.6,0,1,NULL,1,NULL,31.9,1,174,10.4,1,1,1,0,1,1,0,0,0,0,0,0,0
-bph00031,99,BPH,TURP,58,unknown,15,7,36,25,0.78,0,1,NULL,1,NULL,35.2,0,NULL,NULL,0,0,1,0,1,1,0,0,0,0,0,0,0
-bph00032,100,BPH,Simple,63,Cauc,NULL,NULL,NULL,100,11.2,1,0,NULL,0,NULL,28.5,1,140,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00033,102,BPH,TURP,69,Hisp,NULL,5,40,55,14.14,1,1,4,1,6,24.8,1,123,5.9,0,0,1,0,1,1,0,0,0,0,0,0,0
-bph00034,103,BPH,Simple,73,Cauc,6,12.1,0,110,0.84,0,1,24,0,NULL,31.2,0,NULL,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00035,104,BPH,Simple,62,Cauc,26,NULL,NULL,66,2.2,0,0,NULL,1,NULL,35.6,1,145,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00036,106,BPH,TURP,59,Cauc,NULL,50,111,NULL,2.43,1,1,NULL,1,NULL,30.3,0,103,NULL,1,0,1,0,0,1,0,0,0,0,0,0,0
-bph00037,107,BPH,TURP,81,Hisp,NULL,NULL,848,34,15.9,1,1,60,1,60,25.8,1,199,6.3,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00038,108,BPH,TURP,44,Hisp,NULL,10,127,NULL,1.55,0,0,NULL,1,NULL,32.9,1,111,5.5,0,0,1,0,1,1,0,1,0,0,0,0,0
-bph00039,109,BPH,Simple,63,Cauc,NULL,9.1,62,107,4.5,0,1,1,0,NULL,25,0,101,NULL,0,0,0,0,0,1,1,1,1,0,0,0,0
-bph00040,110,BPH,Simple,69,AA,NULL,NULL,NULL,110,2.06,0,1,NULL,1,NULL,32.4,1,143,6.7,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00041,111,BPH,TURP,66,Hisp,NULL,NULL,NULL,72,4.4,1,1,NULL,1,NULL,29.3,1,117,5.7,1,0,1,0,1,1,0,0,0,0,0,0,0
-bph00042,112,BPH,TURP,64,Hisp,NULL,NULL,NULL,58,3.59,1,1,1,1,NULL,30.3,1,200,8.1,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00043,113,BPH,TURP,67,Hisp,NULL,NULL,NULL,81,11.84,1,0,NULL,1,NULL,23.7,0,84,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00044,114,BPH,Simple,69,AA,19,7.5,141,250,6.5,0,0,NULL,1,NULL,23.7,1,183,NULL,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00045,116,BPH,Simple,60,Cauc,10,2.7,377,106,7.7,0,0,NULL,1,NULL,31.8,0,97,NULL,0,0,0,0,0,1,1,1,1,0,0,0,0
-bph00046,117,BPH,TURP,52,Asian,NULL,NULL,NULL,74,2.6,1,0,NULL,1,NULL,24.1,0,NULL,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00047,118,BPH,Simple,77,Cauc,9,NULL,310,155,4.9,1,0,NULL,1,NULL,22.9,1,197,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00048,120,BPH,TURP,73,Hisp,NULL,NULL,NULL,31,2.1,0,1,NULL,1,NULL,26.8,0,114,NULL,0,0,1,0,1,1,0,1,0,0,0,0,0
-bph00049,121,BPH,Simple,61,unknown,NULL,NULL,NULL,91,2.01,1,1,5,1,5,24.9,0,182,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00050,122,BPH,Simple,62,Cauc,NULL,6.6,257,176,18.7,0,0,NULL,0,NULL,25.5,0,106,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00051,123,BPH,Simple,66,Cauc,33,9.3,58,95.6,2.1,0,0,NULL,1,NULL,30.1,1,168,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00052,124,BPH,Simple,70,Cauc,NULL,NULL,NULL,130,6.7,1,0,NULL,0,NULL,30.1,0,99,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00053,125,BPH,TURP,68,Cauc,20,NULL,NULL,55,4.4,0,0,NULL,1,NULL,21.6,1,200,7.8,1,1,1,0,1,1,0,0,0,0,0,0,0
-bph00054,126,BPH,TURP,50,Hisp,NULL,6,18,NULL,0.3,0,1,NULL,1,NULL,29.8,0,111,NULL,1,0,1,0,1,1,0,1,0,0,0,0,0
-bph00055,127,BPH,Simple,66,Cauc,NULL,NULL,NULL,56,5.6,0,0,NULL,0,NULL,27.9,1,187,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00056,128,BPH,Simple,62,Cauc,26,3,396,168,10.8,0,0,NULL,1,NULL,29.4,1,226,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00057,130,BPH,TURP,61,Hisp,NULL,NULL,NULL,54,8.98,0,1,6,1,6,21.8,0,103,NULL,0,1,1,0,1,1,0,1,0,0,0,0,0
-bph00058,131,BPH,TURP,63,Hisp,NULL,NULL,NULL,51.5,2.34,1,1,12,1,12,29.8,1,208,10.3,1,1,1,1,1,1,0,1,0,0,0,0,0
-bph00059,132,BPH,Simple,61,Cauc,NULL,NULL,281,86,2.01,0,1,NULL,1,NULL,24.3,1,178,NULL,1,1,1,1,1,1,1,1,1,0,0,0,0
-bph00060,133,BPH,TURP,79,Hisp,NULL,NULL,227,78,NULL,1,0,NULL,1,9,22.1,1,213,NULL,0,1,1,0,1,1,0,0,0,0,0,0,0
-bph00061,135,BPH,TURP,79,Asian,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,1,NULL,NULL,1,186,8.1,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00062,136,BPH,TURP,63,Cauc,NULL,8,123,36,0.66,0,0,NULL,1,NULL,30.8,0,NULL,NULL,1,1,0,0,0,1,0,0,0,0,0,0,0
-bph00063,137,BPH,Simple,65,Cauc,NULL,22,231,40,6.3,0,0,NULL,0,NULL,28.5,0,98,NULL,0,0,0,0,0,1,0,1,0,0,0,0,0
-bph00064,138,BPH,Simple,56,AA,27,NULL,107,150,0.57,0,1,6,1,6,21.2,0,91,NULL,0,1,1,1,1,1,1,1,1,0,0,0,0
-bph00065,139,BPH,Simple,68,Asian,19,30.7,176,175,6.4,0,1,NULL,0,NULL,32,1,186,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00066,141,BPH,Simple,71,Cauc,NULL,17.8,177,150,3.05,0,1,6,1,6,35.9,0,95,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00067,142,BPH,Simple,77,Cauc,NULL,8.9,151,104,6.5,0,0,NULL,1,24,27.8,1,143,NULL,1,1,1,0,1,1,1,1,0,0,0,0,0
-bph00068,143,BPH,TURP,62,Hisp,NULL,13,60,63,3.12,0,0,NULL,0,NULL,27,0,114,NULL,1,1,1,0,1,1,0,1,0,0,0,0,0
-bph00069,145,BPH,Simple,65,Cauc,NULL,12.1,NULL,135,3.8,1,1,NULL,1,NULL,34.2,1,108,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00070,147,BPH,Simple,66,Cauc,NULL,NULL,62,162,NULL,1,1,NULL,1,NULL,33.7,1,157,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00071,148,BPH,TURP,47,Cauc,NULL,11,0,50,3.76,0,1,NULL,1,NULL,23.9,1,186,8.1,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00072,149,BPH,TURP,80,Hisp,18,13,13,NULL,1.8,0,1,3,1,3,28.5,0,141,NULL,1,1,1,0,1,0,0,1,0,0,0,0,0
-bph00073,150,BPH,TURP,57,Cauc,NULL,7,70,NULL,12.52,0,1,3,1,3,33.2,0,118,NULL,1,1,1,0,1,1,1,1,0,0,0,0,0
-bph00074,151,BPH,TURP,69,AA,13,NULL,67,80,6.4,0,1,5,1,5,31.4,0,111,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00075,152,BPH,Simple,55,Hisp,12,22.7,109,124,2.9,0,0,NULL,0,NULL,32.9,0,89,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00076,153,BPH,TURP,63,Cauc,27,6.8,230,52,6.3,0,1,3,0,NULL,33.9,0,106,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00077,154,BPH,TURP,63,Hisp,NULL,NULL,NULL,30,1.2,0,0,NULL,1,NULL,29.7,0,96,NULL,0,0,1,0,1,1,1,1,0,0,0,0,0
-bph00078,155,BPH,TURP,60,AA,NULL,NULL,NULL,54,3.8,0,1,3,0,NULL,33.5,0,133,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00079,156,BPH,Simple,56,Cauc,27,16.4,18,104,3.9,0,1,2,1,7,26.7,0,81,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00080,157,BPH,Simple,58,Cauc,NULL,NULL,NULL,200,19,1,0,NULL,0,NULL,27.3,0,84,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00081,158,BPH,Simple,69,Cauc,22,NULL,53,141,3,1,0,NULL,1,2,28.1,0,113,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00082,159,BPH,Simple,77,Cauc,NULL,NULL,NULL,237,NULL,1,0,NULL,1,36,31.1,0,106,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00083,160,BPH,Simple,70,Hisp,NULL,NULL,114,104,14.23,1,0,NULL,1,6,26.4,0,125,NULL,1,0,1,1,1,1,1,1,1,0,0,0,0
-bph00084,161,BPH,Simple,59,Hisp,NULL,8,122,202,11.75,0,0,NULL,0,NULL,28.9,0,115,NULL,1,0,1,1,1,1,1,1,1,0,0,0,0
-bph00085,162,BPH,Simple,63,Hisp,NULL,11,31,93,1.38,0,1,6,1,6,42.7,1,135,NULL,1,1,1,1,1,1,1,1,1,0,0,0,0
-bph00086,163,BPH,Simple,70,Cauc,NULL,4.7,NULL,165,7.4,0,0,NULL,0,NULL,36.2,0,137,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00087,164,BPH,Simple,77,AA,15,4.8,81,156,11.11,0,1,9,1,1,27.6,0,98,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00088,165,BPH,Simple,63,Hisp,NULL,NULL,NULL,100,12.75,1,1,3,1,3,29.2,1,252,10.4,0,1,1,1,1,1,1,1,1,0,0,0,0
-bph00089,166,BPH,Simple,72,Hisp,20,6.2,0,113,10.46,0,1,0.5,1,13,30.9,1,222,8,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00090,167,BPH,TURP,62,AA,34,NULL,NULL,81,3.59,0,1,12,1,12,36.6,0,NULL,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00091,168,BPH,TURP,81,Hisp,NULL,NULL,92,90,3.53,1,1,12,1,NULL,22.9,0,NULL,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00092,169,BPH,Simple,56,Hisp,15,NULL,NULL,118,6.14,1,0,NULL,1,6,35.3,1,217,6.8,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00093,170,BPH,Simple,69,unknown,15,0,270,100,4.93,0,0,NULL,1,NULL,26.6,0,186,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00094,171,BPH,Simple,82,Cauc,4,12.7,103,200,6.7,0,1,NULL,1,NULL,27.7,0,99,NULL,1,1,0,0,0,1,1,1,1,0,0,0,0
-bph00095,172,BPH,Simple,79,Cauc,24,NULL,72,243,2.56,0,1,2,1,2,27,0,105,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00096,173,BPH,Simple,68,Cauc,NULL,48.6,147,108,2.1,0,1,8,1,8,31.7,0,97,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00097,174,BPH,Simple,72,Cauc,5,NULL,NULL,150,NULL,1,1,4,1,NULL,23.7,0,91,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00098,175,BPH,TURP,59,Hisp,28,NULL,NULL,25,0.91,0,1,NULL,1,NULL,27,0,110,NULL,0,1,1,0,1,1,1,1,0,0,0,0,0
-bph00099,176,BPH,Simple,62,Cauc,12,8.6,700,109,29.06,0,0,NULL,1,6,29.9,0,104,NULL,1,1,0,0,1,1,1,1,1,0,0,0,0
-bph00100,177,BPH,Simple,73,Cauc,14,5.4,293,112,5.2,0,1,24,1,24,26.6,0,93,NULL,0,0,0,0,0,1,1,1,1,0,0,0,0
-bph00101,178,BPH,Simple,69,Cauc,NULL,NULL,NULL,120,13,1,0,NULL,1,3,27.4,0,96,NULL,0,0,0,0,0,1,1,1,1,0,0,0,0
-bph00102,179,BPH,Simple,83,Cauc,12,7,50,156,18.7,0,0,NULL,0,NULL,33.7,0,162,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00103,180,BPH,Simple,67,Cauc,19,3.8,118,93,6.7,0,0,NULL,0,NULL,27.9,0,94,NULL,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00104,181,BPH,Simple,70,Cauc,18,8.9,29,227,7.5,0,1,108,0,NULL,24.4,0,92,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00105,182,BPH,Simple,65,Hisp,7,15.5,282,200,10.2,0,0,NULL,0,NULL,26.6,1,190,9.5,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00106,183,BPH,TURP,78,Hisp,24,NULL,178,120,10.78,0,1,5,1,5,31.2,1,169,7.8,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00107,184,BPH,TURP,66,Hisp,NULL,2,NULL,32,1.06,0,1,3,1,3,30.7,0,NULL,NULL,0,1,1,1,1,1,1,1,1,0,0,0,0
-bph00108,185,BPH,Simple,57,Hisp,NULL,14,111,81,8.89,0,1,3,1,9,28.3,1,126,6,0,0,1,1,1,1,1,1,1,0,0,0,0
-bph00109,186,BPH,Simple,70,Cauc,NULL,0,300,99,NULL,1,1,2,1,2,24.3,0,99,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00110,187,BPH,Simple,72,Cauc,14,7.3,18,170,8.7,1,0,NULL,1,15,27.7,0,71,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00111,188,BPH,Simple,74,Cauc,31,6,220,200,3.4,0,0,NULL,1,9,30.2,0,97,NULL,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00112,189,BPH,TURP,66,AA,NULL,4,113,27,0.52,1,1,5,1,4,21.9,0,119,NULL,0,1,1,0,1,0,0,1,0,0,0,0,0
-bph00113,190,BPH,Simple,52,Hisp,NULL,NULL,NULL,96,5.49,1,1,12,1,12,23.9,0,114,NULL,1,1,1,1,1,1,1,1,1,0,0,0,0
-bph00114,191,BPH,TURP,73,Hisp,NULL,NULL,NULL,65,5.04,0,1,12,1,12,27.6,0,90,NULL,1,1,1,1,1,1,1,1,1,0,0,0,0
-bph00115,192,BPH,Simple,62,Cauc,17,25,NULL,120,6.7,1,0,NULL,0,NULL,31.4,0,100,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00116,193,BPH,Simple,75,Cauc,10,NULL,593,328,19.6,1,0,NULL,0,NULL,22.9,0,105,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00117,194,BPH,Simple,61,Cauc,9,6.7,264,150,NULL,0,0,NULL,0,NULL,30.6,1,130,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00118,195,BPH,Simple,64,Cauc,26,8.3,160,136,2.6,0,0,NULL,1,NULL,25.2,0,117,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00119,196,BPH,Simple,60,Cauc,21,2.1,NULL,138,7.5,0,0,NULL,0,NULL,25.1,0,312,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00120,197,BPH,Simple,47,Cauc,29,12.7,27,104,10,0,0,NULL,1,3,34.6,0,104,NULL,0,0,1,0,1,1,1,1,1,0,0,0,0
-bph00121,198,BPH,Simple,70,Hisp,17,12.5,181,132,4.6,1,1,2,1,2,29.8,0,160,NULL,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00122,199,BPH,Simple,78,Cauc,22,2.8,534,100,2,0,0,NULL,0,NULL,25.1,1,231,7,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00123,200,BPH,Simple,62,Cauc,NULL,NULL,88,130,11.24,1,0,NULL,1,4,27.8,0,99,NULL,0,0,1,0,0,1,1,1,1,0,0,0,0
-bph00124,203,BPH,Simple,72,Cauc,8,9.9,61,95,10.42,0,0,NULL,0,NULL,27.1,0,77,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00125,204,BPH,Simple,62,Cauc,22,NULL,NULL,140,12.21,0,0,NULL,0,NULL,33.7,0,137,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00126,205,BPH,Simple,70,Cauc,19,NULL,11,220,5.88,0,0,NULL,0,NULL,21.6,0,110,NULL,1,0,1,1,0,1,1,1,1,0,0,0,0
-bph00127,206,BPH,Simple,72,Cauc,23,8.6,404,120,2,0,1,6,1,3,35.2,0,123,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00128,207,BPH,Simple,64,Cauc,25,11.9,113,96,4.3,0,0,NULL,1,NULL,28.5,0,83,NULL,0,1,1,1,0,1,1,1,1,0,0,0,0
-bph00129,208,BPH,Simple,68,Cauc,21,9.3,25,102,6.5,0,0,NULL,0,NULL,33.8,0,122,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00130,209,BPH,Simple,90,Cauc,NULL,2.7,119,220,9.21,1,1,9,0,NULL,26.3,0,105,NULL,0,1,1,0,0,1,1,1,1,0,0,0,0
-bph00131,210,BPH,TURP,60,Hisp,NULL,NULL,50,51,2.7,0,1,3,1,3,30.9,0,94,NULL,1,1,1,0,0,0,0,0,0,0,0,0,0
-bph00132,211,BPH,Simple,70,AA,19,28.2,73,150,3.34,0,1,9,1,9,38.8,1,118,5.2,1,1,1,1,0,0,0,0,0,0,0,0,0
-bph00133,212,BPH,TURP,NULL,unknown,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,0,0,0,0,0,0,0,0,0,0
-bph00134,213,BPH,Simple,65,Cauc,9,16,9,100,1.68,0,0,NULL,0,NULL,24.4,1,178,NULL,0,1,0,0,0,1,1,1,1,0,0,0,0
-bph00135,214,BPH,Simple,63,Hisp,NULL,NULL,NULL,114,3.32,1,1,5,1,5,27.2,0,101,NULL,1,0,1,0,0,1,1,1,1,0,0,0,0
-bph00136,215,BPH,Simple,75,Cauc,11,21.6,111,103,4.3,0,0,NULL,0,NULL,22.2,0,101,NULL,1,1,1,0,0,1,1,1,1,0,0,0,0
-bph00137,216,BPH,Simple,51,AA,28,8.1,83,140,5.32,1,0,NULL,1,NULL,29.1,0,108,NULL,0,0,0,0,0,1,1,1,1,1,0,0,0
-bph00138,217,BPH,Simple,75,Cauc,20,5.2,95,120,5.38,0,0,NULL,0,NULL,32.3,0,124,NULL,0,0,1,0,0,1,1,1,1,1,0,0,0
-bph00139,218,BPH,Simple,82,Cauc,10,NULL,NULL,350,8.44,1,0,NULL,0,NULL,35,1,201,NULL,1,1,1,0,0,1,1,1,1,1,0,0,0
-bph00140,219,BPH,Simple,68,Cauc,12,11,94,120,20,0,1,NULL,1,NULL,27.1,1,196,NULL,0,1,1,1,0,1,1,1,1,0,0,0,0
-bph00141,221,BPH,TURP,62,Cauc,NULL,NULL,NULL,NULL,0.88,1,0,NULL,1,6,28.9,0,NULL,NULL,0,0,1,0,0,0,1,1,1,0,0,0,0
-bph00142,222,BPH,Simple,60,Cauc,14,6.1,89,134,6,0,1,6,1,NULL,23.7,1,182,NULL,1,0,1,0,0,1,1,1,1,1,0,0,0
-bph00143,223,BPH,Simple,70,Cauc,32,NULL,428,119,7.85,1,0,NULL,1,NULL,35.9,1,209,7.3,0,1,1,1,0,1,1,1,1,0,0,0,0
-bph00144,224,BPH,Simple,75,Cauc,14,4.6,111,157,13.7,0,0,NULL,1,12,31.3,0,123,NULL,1,1,1,1,0,0,1,1,1,0,0,0,0
-bph00145,225,BPH,Simple,73,Cauc,9,8,137,130,1.8,1,1,9,1,9,30.2,1,191,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00146,226,BPH,Simple,NULL,unknown,17,NULL,NULL,NULL,NULL,NULL,0,NULL,1,4,30,0,NULL,NULL,0,0,1,1,0,0,0,0,0,0,0,0,0
-bph00147,227,BPH,Simple,63,Hisp,NULL,NULL,NULL,113,6.7,1,0,NULL,1,12,26.8,1,192,6.3,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00148,228,BPH,Simple,70,Cauc,21,8,63,142,2.8,0,0,NULL,0,NULL,35.3,1,217,NULL,0,1,1,0,0,1,1,1,0,1,0,0,0
-bph00149,230,BPH,Simple,82,Cauc,25,12.5,58,124,NULL,0,1,NULL,0,NULL,24,1,207,NULL,1,1,1,1,0,1,1,1,1,1,0,0,0
-bph00150,231,BPH,Simple,65,unknown,35,5.9,871,110,8.11,1,0,NULL,0,NULL,24.2,0,99,NULL,0,0,1,0,0,1,0,1,1,1,0,0,0
-bph00151,232,BPH,Simple,71,Cauc,11,NULL,178,178,6.4,0,0,NULL,1,NULL,36.1,0,108,NULL,1,1,1,0,0,1,1,1,1,1,0,0,0
-bph00152,233,BPH,Simple,72,Hisp,29,7,35,105,4.27,1,1,6,1,6,22.1,0,103,NULL,1,0,1,0,0,1,1,1,1,0,0,0,0
-bph00153,234,BPH,Simple,58,Hisp,NULL,5.8,117,100,4.9,1,0,NULL,1,6,27.2,0,96,NULL,0,0,1,0,0,1,1,1,1,1,0,0,0
-bph00154,235,BPH,Simple,79,Cauc,19,1.9,138,105,1.9,0,1,84,1,84,27.1,0,114,NULL,1,1,1,1,0,1,0,1,1,0,0,0,0
-bph00155,237,BPH,Simple,67,AA,10,14.3,76,91,11,0,0,NULL,0,NULL,28.7,0,98,NULL,0,1,1,0,0,1,1,1,0,0,0,0,0
-bph00156,238,BPH,Simple,59,Cauc,NULL,NULL,NULL,127,6.17,0,0,NULL,1,3,35.9,1,158,6.2,1,1,1,0,0,1,1,1,0,0,0,0,0
-bph00157,239,BPH,Simple,78,Hisp,NULL,8.2,30,98,4.5,1,0,NULL,0,NULL,31.9,0,115,NULL,1,1,1,0,0,0,1,1,1,0,0,0,0
-bph00158,241,BPH,Simple,66,Cauc,27,3.8,30,90,3.5,0,1,7,1,2,35.4,0,105,NULL,1,0,1,0,0,1,1,1,1,0,0,0,0
-bph00159,242,BPH,Simple,74,Cauc,19,NULL,79,NULL,NULL,1,0,NULL,1,3,19,0,83,NULL,0,0,1,0,0,1,1,1,0,1,0,0,0
-bph00160,243,BPH,Simple,56,Hisp,NULL,NULL,746,190,6.67,1,1,12,1,14,35.1,1,211,7.9,1,1,1,0,0,1,1,1,1,0,0,0,0
-bph00161,244,BPH,Simple,76,Cauc,10,7.3,72,175,5.17,0,0,NULL,0,NULL,18.5,1,132,NULL,1,0,1,1,0,1,1,1,0,1,0,0,0
-bph00162,245,BPH,Simple,63,AA,NULL,NULL,NULL,123,2.7,1,1,12,1,3,33.5,0,NULL,NULL,0,0,1,0,0,1,1,1,0,0,0,0,0
-bph00163,246,BPH,Simple,61,Cauc,NULL,NULL,NULL,120,18.52,1,1,3,1,3,28.5,1,247,10.1,0,1,1,0,0,1,1,1,1,0,0,0,0
-bph00164,247,BPH,Simple,78,Hisp,NULL,NULL,NULL,117,NULL,1,1,3,1,3,23.9,0,162,NULL,0,1,0,0,0,1,1,1,0,0,0,0,0
-bph00165,249,BPH,Simple,60,Hisp,NULL,NULL,NULL,112,3.08,1,1,6,1,12,29.2,1,140,6.5,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00166,250,BPH,Simple,63,Cauc,NULL,NULL,NULL,119,4.9,1,0,NULL,1,NULL,29.5,0,99,NULL,0,0,1,0,0,1,1,1,1,1,0,0,0
-bph00167,251,BPH,Simple,64,Hisp,27,NULL,293,99,6.54,0,1,9,1,9,31.8,0,114,NULL,1,0,1,0,1,1,1,1,1,0,0,0,0
-bph00168,252,BPH,Simple,63,Cauc,17,11.5,380,104,NULL,0,0,NULL,0,NULL,33.3,1,131,NULL,1,0,1,1,0,0,0,1,1,1,0,0,0
-bph00169,254,BPH,Simple,60,Cauc,28,8.9,354,130,4.2,0,0,NULL,0,NULL,28.1,0,91,NULL,1,0,1,1,0,1,1,1,1,1,0,0,0
-bph00170,255,BPH,Simple,61,Hisp,10,9.3,120,96,8.47,1,1,NULL,1,NULL,34.8,0,166,NULL,0,0,1,0,0,1,1,1,1,0,0,0,0
-bph00171,256,BPH,Simple,69,Cauc,23,7,166,110,6.95,0,1,6,1,6,28.2,1,359,7.1,1,1,1,1,1,0,1,1,1,1,0,0,0
-bph00172,257,BPH,Simple,72,Cauc,NULL,10.8,54,112,1.7,1,0,NULL,1,36,39.6,1,219,NULL,1,1,1,0,0,1,1,1,1,1,0,0,0
-bph00173,258,BPH,Simple,65,Cauc,NULL,NULL,NULL,200,NULL,0,0,NULL,0,NULL,25.7,0,86,NULL,0,0,1,0,0,1,1,1,1,0,0,0,0
-bph00174,259,BPH,Simple,66,Cauc,19,NULL,555,132,19,0,0,NULL,0,NULL,23.7,0,106,NULL,0,0,1,0,0,1,1,1,1,0,0,0,0
-bph00175,260,BPH,Simple,61,Cauc,30,7.3,45,125,3.39,0,0,NULL,1,36,28.9,0,181,NULL,1,0,1,1,0,1,1,1,1,0,0,0,0
-bph00176,261,BPH,Simple,67,Cauc,12,7.4,120,209,12.76,0,0,NULL,0,NULL,32.3,0,123,NULL,1,1,1,1,0,1,1,1,1,0,0,0,0
-bph00177,262,BPH,Simple,67,Cauc,31,NULL,53,120,17.6,1,1,36,1,36,32.9,0,106,NULL,1,1,1,1,0,0,1,1,1,0,0,0,0
-bph00178,263,BPH,Simple,65,Cauc,21,NULL,NULL,116,10.8,1,1,6,1,6,23.7,0,110,NULL,0,0,1,0,0,0,1,1,1,1,0,0,0
-bph00179,265,BPH,Simple,66,Cauc,3,NULL,67,125,9.5,0,0,NULL,0,NULL,21.1,0,104,NULL,0,0,1,1,0,0,1,1,1,1,0,0,0
-bph00180,266,BPH,Simple,78,Cauc,14,12,526,134,9.27,0,0,NULL,1,2,26.9,0,103,NULL,0,0,1,0,0,1,1,1,1,1,0,0,0
-bph00181,267,BPH,Simple,76,Hisp,NULL,NULL,NULL,NULL,NULL,0,0,NULL,1,5,27.2,1,174,7.7,0,0,1,0,1,0,1,1,1,0,0,0,0
-bph00182,269,BPH,Simple,64,Cauc,9,6.8,12,100,5.21,0,0,NULL,0,NULL,35.4,0,106,NULL,0,0,1,1,0,0,1,1,0,0,0,0,0
-bph00183,270,BPH,Simple,71,Cauc,5,5.5,279,106,6.58,0,0,NULL,0,NULL,29.4,0,114,NULL,1,0,1,1,1,1,1,1,1,1,0,0,0
-bph00184,271,BPH,Simple,55,Hisp,NULL,5.7,119,85,3.44,1,1,3,1,24,38,1,144,6,1,1,1,0,1,0,1,1,1,0,0,0,0
-bph00185,272,BPH,Simple,68,Cauc,10,8.4,NULL,105,3.1,0,0,NULL,0,NULL,33.2,1,176,NULL,1,1,1,0,1,1,1,1,1,0,0,0,0
-bph00186,273,BPH,Simple,74,Hisp,NULL,9.7,31,170,NULL,0,0,NULL,1,3,31.9,0,111,NULL,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00187,274,BPH,Simple,75,Cauc,10,NULL,NULL,100,NULL,1,0,NULL,0,NULL,20.6,0,97,NULL,1,0,0,0,1,1,1,1,1,1,0,0,0
-bph00188,275,BPH,Simple,67,Asian,17,11.5,73,130,5.86,0,1,6,0,NULL,26.2,0,124,NULL,1,0,1,0,1,0,1,1,1,1,0,0,0
-bph00189,276,BPH,Simple,66,Cauc,16,5,121,102.3,5.87,0,0,NULL,1,NULL,27.1,0,99,NULL,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00190,277,BPH,Simple,75,Cauc,NULL,NULL,NULL,182,9.8,1,1,6,1,6,29.7,1,142,NULL,0,1,1,0,1,0,1,1,1,1,0,0,0
-bph00191,278,BPH,Simple,78,Cauc,26,NULL,173,198,NULL,1,0,NULL,1,2,25.1,0,102,NULL,0,1,1,0,1,1,1,1,1,1,0,0,0
-bph00192,279,BPH,Simple,81,Cauc,NULL,3.3,NULL,165,NULL,0,0,NULL,0,NULL,24.1,1,261,NULL,0,1,1,0,1,1,1,1,1,1,0,0,0
-bph00193,280,BPH,Simple,73,Cauc,16,NULL,NULL,120,1.9,1,1,12,0,NULL,30.1,0,165,NULL,1,0,1,0,1,1,1,1,1,1,0,0,0
-bph00194,281,BPH,Simple,64,Cauc,29,4.4,223,152,9.93,0,0,NULL,1,2,26.2,0,116,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00195,282,BPH,Simple,62,Cauc,21,8.2,501,149,2.54,0,1,12,1,12,25.1,0,108,NULL,1,0,1,0,1,0,1,1,1,1,0,0,0
-bph00196,283,BPH,Simple,81,Cauc,NULL,2,500,127,NULL,1,0,NULL,1,9,24.4,0,91,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00197,284,BPH,Simple,70,AA,NULL,NULL,NULL,120,3.62,1,1,12,1,12,29.6,1,194,6.5,0,1,1,0,1,1,1,1,1,0,0,0,0
-bph00198,285,BPH,Simple,73,Hisp,35,8.3,85,100,1.01,0,0,NULL,1,12,35.4,1,213,NULL,0,1,1,0,1,1,1,1,1,1,0,0,0
-bph00199,286,BPH,Simple,70,Cauc,24,9.9,70,95,NULL,0,0,NULL,1,3,27.3,0,93,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00200,287,BPH,Simple,82,Cauc,33,25,189,81,6.85,0,1,84,1,3,27.3,1,200,NULL,1,1,1,1,1,1,1,1,1,1,0,0,0
-bph00201,288,BPH,Simple,57,Cauc,NULL,NULL,NULL,99,NULL,0,0,NULL,0,NULL,30.6,0,118,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00202,289,BPH,Simple,61,Cauc,20,6.2,205,82,11.61,0,1,3,1,3,31.6,1,239,NULL,1,1,1,1,1,1,1,1,1,1,0,0,0
-bph00203,290,BPH,Simple,60,Cauc,10,9.8,177,236,12,0,0,NULL,0,NULL,29.4,0,88,NULL,0,0,1,1,1,1,1,1,1,1,0,0,0
-bph00204,291,BPH,Simple,55,Cauc,30,8.5,186,92,1.41,0,0,NULL,1,6,28.4,0,132,NULL,0,0,1,1,1,0,1,1,0,1,0,0,0
-bph00205,292,BPH,Simple,71,Cauc,18,14.1,112,120,7.53,1,0,NULL,0,NULL,22.5,0,87,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00206,293,BPH,Simple,70,Cauc,NULL,NULL,NULL,300,4.9,0,1,NULL,1,NULL,31,0,103,NULL,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00207,294,BPH,Simple,84,Cauc,7,4.7,61,140,6.73,0,0,NULL,0,NULL,26.8,1,124,6.1,0,1,1,0,1,1,1,1,1,1,0,0,0
-bph00208,295,BPH,Simple,76,AA,12,NULL,NULL,106,NULL,1,0,NULL,0,NULL,22.3,0,128,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00209,296,BPH,Simple,66,Cauc,22,9,150,177,13,0,0,NULL,0,NULL,26.9,0,92,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00210,297,BPH,Simple,74,Hisp,5,15.1,82,100,7.62,0,1,15,1,15,26.2,0,99,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00211,298,BPH,Simple,65,Cauc,15,9.5,NULL,148,4.1,0,1,12,0,NULL,28,0,94,NULL,0,1,1,0,1,1,1,1,1,1,0,0,0
-bph00212,299,BPH,Simple,68,AA,16,NULL,452,151,6.29,1,0,NULL,1,15,32.1,1,256,6.2,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00213,300,BPH,Simple,65,Cauc,NULL,5.8,82,NULL,2.61,0,0,NULL,0,NULL,25.1,0,103,NULL,0,0,1,0,1,1,1,1,1,1,0,0,0
-bph00214,301,BPH,Simple,62,Hisp,NULL,NULL,NULL,186,6.6,1,1,2,1,2,32.9,0,138,NULL,0,1,1,1,1,0,1,1,1,0,0,0,0
-bph00215,302,BPH,Simple,76,Cauc,6,5.8,NULL,150,2.16,0,1,60,0,NULL,25.1,0,84,NULL,1,0,1,0,1,0,1,1,1,1,0,0,0
-bph00216,303,BPH,Simple,53,Hisp,NULL,NULL,151,173,15.6,1,0,NULL,1,6,27.1,0,91,NULL,0,0,1,0,1,0,1,1,1,0,0,0,0
-bph00217,304,BPH,Simple,69,Hisp,16,NULL,93,100,5.28,0,0,NULL,1,12,29.1,0,108,NULL,0,1,0,0,0,0,1,1,1,0,0,0,0
-bph00218,305,BPH,Simple,75,Asian,10,8.6,54,100,7.16,0,0,NULL,0,NULL,23,0,98,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00219,306,BPH,Simple,81,Hisp,8,NULL,NULL,125,NULL,0,1,36,0,NULL,27.1,1,169,NULL,1,1,1,0,1,0,1,1,1,1,0,0,0
-bph00220,307,BPH,Simple,68,Cauc,14,4.1,365,84,4.5,0,0,NULL,1,6,28.5,0,99,NULL,1,0,1,0,1,0,1,1,1,1,0,0,0
-bph00221,308,BPH,Simple,70,Cauc,23,NULL,NULL,115,6.77,0,0,NULL,1,NULL,27.8,1,142,7,1,1,1,0,1,0,1,1,1,1,0,0,0
-bph00222,309,BPH,Simple,71,Cauc,13,11,188,107,8.2,0,1,60,1,60,24,0,89,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00223,310,BPH,Simple,62,Cauc,5,10.8,96,131,6.9,0,0,NULL,0,NULL,25.5,0,140,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00224,311,BPH,Simple,79,Cauc,NULL,NULL,NULL,100,3,1,1,30,1,30,30.3,0,111,NULL,0,0,0,0,0,0,0,0,0,0,0,0,0
-bph00225,312,BPH,Simple,70,Cauc,NULL,10.1,151,130,1.62,1,1,15,1,20,36,0,115,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00226,313,BPH,Simple,79,Cauc,NULL,NULL,NULL,110,NULL,0,1,6,1,6,31.4,1,212,7,1,1,1,0,1,0,1,1,1,1,0,0,0
-bph00227,314,BPH,Simple,76,Cauc,7,10.2,68,143,10.49,0,0,NULL,0,NULL,25.1,0,146,NULL,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00228,315,BPH,Simple,68,Hisp,NULL,NULL,NULL,300,4.51,0,1,6,1,6,29.1,1,209,8.9,1,1,1,0,1,0,1,1,1,0,0,0,0
-bph00229,316,BPH,Simple,37,AA,NULL,NULL,701,140,0.8,1,0,NULL,1,NULL,29.1,0,116,NULL,1,1,1,0,1,1,1,1,1,1,0,0,0
-bph00230,317,BPH,Simple,68,Cauc,24,7,137,95,21.03,0,1,24,1,24,24.3166324831,0,123,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00231,318,BPH,Simple,59,AA,NULL,NULL,NULL,98,7.21,1,1,3,1,3,21.9939045465,0,95,NULL,0,0,1,0,1,0,1,1,1,0,0,0,0
-bph00232,319,BPH,Simple,82,Cauc,NULL,NULL,NULL,100,NULL,1,0,NULL,1,3,30.3434423835,1,93,NULL,1,1,0,0,1,0,1,1,1,1,0,0,0
-bph00233,320,BPH,Simple,64,Cauc,20,NULL,307,144,9.8,0,0,NULL,1,48,26.8667204001,0,103,NULL,1,0,0,0,0,0,1,1,1,1,0,0,0
-bph00234,321,BPH,Simple,73,Cauc,22,NULL,NULL,130,NULL,1,1,3,0,NULL,45.2122054443,1,264,NULL,1,1,0,0,1,0,1,1,1,1,0,0,0
-bph00235,322,BPH,Simple,71,Hisp,NULL,NULL,NULL,114,6,1,1,9,1,9,28.3415792025,0,131,NULL,1,1,1,1,1,0,1,1,1,0,0,0,0
-bph00236,324,BPH,Simple,70,AA,35,3.3,67,119,5.39,0,0,NULL,1,NULL,25.6184830928,1,148,NULL,1,1,1,0,1,0,1,1,1,0,0,0,0
-bph00237,325,BPH,Simple,76,Cauc,23,NULL,150,300,7.8,0,0,NULL,0,NULL,21.5023398791,0,119,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00238,326,BPH,Simple,68,Cauc,14,11,74,185,4.91,0,1,6,1,6,29.7034081242,0,111,NULL,0,0,1,0,1,0,1,1,1,1,0,0,0
-bph00239,327,BPH,Simple,74,Cauc,NULL,NULL,NULL,144,21,1,0,NULL,0,NULL,26.6289210018,0,118,NULL,1,1,1,0,1,1,1,1,0,0,0,0,0
-bph00240,328,BPH,Simple,69,Hisp,24,3.8,32,165,8.6,1,0,NULL,0,NULL,31.7278602178,1,126,NULL,1,1,1,0,1,0,1,1,1,1,0,0,0
-bph00241,329,BPH,Simple,68,Cauc,16,12.6,79,115,5.9,0,0,NULL,1,NULL,25.8122965226,0,123,NULL,1,0,0,0,1,0,1,1,1,1,0,0,0
-bph00242,330,BPH,Simple,78,Cauc,NULL,4.3,213,130,NULL,1,1,NULL,1,NULL,24.3888637392,1,183,NULL,0,1,1,0,1,0,1,1,1,0,0,0,0
-bph00243,331,BPH,Simple,59,AA,NULL,NULL,NULL,104,2.77,1,1,4,1,2,23.6901356293,0,NULL,NULL,0,1,1,0,1,1,1,1,0,0,0,0,0
-bph00244,332,BPH,Simple,71,Cauc,13,15.6,239,140,7.81,0,0,NULL,1,4,29.5579457926,1,128,NULL,1,1,1,0,1,0,1,1,1,1,0,0,0
-bph00245,333,BPH,Simple,61,Cauc,30,NULL,NULL,90,1.38,0,0,NULL,0,NULL,23.7394525263,0,118,NULL,0,0,1,0,1,0,0,0,0,1,0,0,0
-bph00246,334,BPH,Simple,70,Hisp,NULL,NULL,NULL,120,5.6,1,0,NULL,1,5,26.5398489981,1,177,NULL,0,1,1,0,1,0,1,1,1,1,0,0,0
-bph00247,335,BPH,Simple,72,Cauc,19,17.9,159,153,3.3,1,1,3,1,3,43.1441275693,1,155,NULL,1,1,0,0,0,0,1,1,1,1,0,0,0
-bph00248,336,BPH,Simple,66,AA,NULL,NULL,29,200,9.17,1,1,12,1,12,27.1131437167,0,87,NULL,0,1,0,0,0,0,1,1,1,1,0,0,0
-bph00249,337,BPH,Simple,68,Cauc,23,9.8,35,113,NULL,0,1,NULL,1,NULL,44.8745838362,0,118,NULL,1,1,0,0,0,0,1,1,1,1,0,0,0
-bph00250,338,BPH,Simple,69,Cauc,21,5.7,171,160,3.24,1,0,NULL,0,NULL,48.8493787239,1,169,NULL,1,1,0,0,0,0,1,1,1,1,0,0,0
-bph00251,D2,Donor,NULL,24,NULL,NULL,NULL,NULL,17,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00252,D3,Donor,NULL,19,NULL,NULL,NULL,NULL,18,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00253,D4,Donor,NULL,24,NULL,NULL,NULL,NULL,15,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00254,D5,Donor,NULL,21,NULL,NULL,NULL,NULL,17,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00255,D6,Donor,NULL,47,NULL,NULL,NULL,NULL,30,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00256,D7,Donor,NULL,18,NULL,NULL,NULL,NULL,16,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00257,D8,Donor,NULL,18,NULL,NULL,NULL,NULL,18,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,0,0,1,1,1,1,1,1,1
-bph00258,D9,Donor,NULL,19,NULL,NULL,NULL,NULL,17,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,1,1,0,1,1,1,1,1,1,1
-bph00259,D10,Donor,NULL,29,NULL,NULL,NULL,NULL,19,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00260,D11,Donor,NULL,40,NULL,NULL,NULL,NULL,30,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00261,D12,Donor,NULL,28,NULL,NULL,NULL,NULL,22,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00262,D13,Donor,NULL,37,NULL,NULL,NULL,NULL,30,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00263,D14,Donor,NULL,22,NULL,NULL,NULL,NULL,16,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00264,D15,Donor,NULL,43,NULL,NULL,NULL,NULL,27,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00265,D16,Donor,NULL,25,NULL,NULL,NULL,NULL,16,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00266,D17,Donor,NULL,31,NULL,NULL,NULL,NULL,23,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00267,D18,Donor,NULL,25,AA,NULL,NULL,NULL,26,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00268,D19,Donor,NULL,51,Hisp,NULL,NULL,NULL,75,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00269,D20,Donor,NULL,18,NULL,NULL,NULL,NULL,20,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00270,D21,Donor,NULL,59,NULL,NULL,NULL,NULL,30,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00271,D22,Donor,NULL,38,NULL,NULL,NULL,NULL,30,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,0,1,0,1,1,1,1,1,1,1
-bph00272,D23,Donor,NULL,NULL,NULL,NULL,NULL,NULL,28,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00273,D24,Donor,NULL,48,NULL,NULL,NULL,NULL,24,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00274,D25,Donor,NULL,32,NULL,NULL,NULL,NULL,16,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00275,D26,Donor,NULL,29,NULL,NULL,NULL,NULL,19,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00276,D27,Donor,NULL,25,NULL,NULL,NULL,NULL,15,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00277,D28,Donor,NULL,22,NULL,NULL,NULL,NULL,14,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,1,1,0,1,1,1,1,1,1,1
-bph00278,D29,Donor,NULL,42,NULL,NULL,NULL,NULL,18,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,1,0,0,1,1,1,1,1,1,1
-bph00279,D31,Donor,NULL,27,NULL,NULL,NULL,NULL,20,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00280,D32,Donor,NULL,23,NULL,NULL,NULL,NULL,18,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00281,D33,Donor,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00282,D34,Donor,NULL,NULL,NULL,NULL,NULL,NULL,19,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00283,D35,Donor,NULL,29,NULL,NULL,NULL,NULL,20,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00284,D36,Donor,NULL,NULL,NULL,NULL,NULL,NULL,21,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00285,D37,Donor,NULL,29,NULL,NULL,NULL,NULL,24,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00286,D38,Donor,NULL,25,NULL,NULL,NULL,NULL,21,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,0,0,0,1,1,1,1,1,1,1
-bph00287,D39,Donor,NULL,32,NULL,NULL,NULL,NULL,20,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00288,D40,Donor,NULL,40,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-bph00289,D41,Donor,NULL,50,NULL,NULL,NULL,NULL,34,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,1,1,1,0,1,1,1,1,1,1,1
-bph00290,D42,Donor,NULL,40,NULL,NULL,NULL,NULL,27,NULL,NULL,NULL,NULL,0,NULL,NULL,0,NULL,NULL,0,0,0,0,0,0,1,1,1,1,1,1,1
-
diff --git a/layouts/custom/contact.html b/layouts/custom/contact.html
index f04f7d1..36f50cb 100644
--- a/layouts/custom/contact.html
+++ b/layouts/custom/contact.html
@@ -7,16 +7,14 @@
<div class="content">
<p style="text-align: center">
- Questions about our research or need a tip on one of our protocols?
- Interested in collaborations? Email us, mention any person, project, or
- activity of interest,and we will get back to you soon!
+ Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us,
+ mention any person, project, or activity of interest,and we will get back to you soon!
</p>
<hr>
<div style="text-align: center">
<iframe
src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3353.0540362781526!2d-96.84412528424524!3d32.81733318923467!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x864e9c04b088e599%3A0x2e63ea34f8b2150b!2sUT%20Southwestern%20Medical%20Center!5e0!3m2!1sen!2sus!4v1576207208811!5m2!1sen!2sus"
- width="600" height="450" frameborder="0" style="border:0"
- allowfullscreen=""></iframe>
+ width="600" height="450" frameborder="0" style="border:0" allowfullscreen=""></iframe>
</div>
<hr>
<div style="text-align: center">
diff --git a/layouts/custom/hu.donor.deep.html b/layouts/custom/hu.donor.deep.html
index 6c253b5..c3c91eb 100644
--- a/layouts/custom/hu.donor.deep.html
+++ b/layouts/custom/hu.donor.deep.html
@@ -160,19 +160,19 @@
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var selectedGene = $("#gene").autocomplete({
- source: genes.genes,
- maxResults: 10,
- maxShowItems: 10,
- minLength: 1,
+ source: genes.genes,
+ maxResults: 10,
+ maxShowItems: 10,
+ minLength: 1,
});
- });
- $("#analysis").click(function (event) {
+ });
+ $("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
- alert("Gene " + _gene + " not exist in the data.")
- return
+ alert("Gene " + _gene + " not exist in the data.")
+ return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
@@ -186,6 +186,6 @@
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
- });
+ });
</script>
</head>
\ No newline at end of file
diff --git a/layouts/custom/hu.donor.shallow.html b/layouts/custom/hu.donor.shallow.html
index 1fdd76b..0e9cf0a 100644
--- a/layouts/custom/hu.donor.shallow.html
+++ b/layouts/custom/hu.donor.shallow.html
@@ -1,191 +1,191 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
<div class="content">
- {{ .Content }}
+ {{ .Content }}
</div>
<style>
- .content {
- margin: 0;
- max-width: none;
- }
-
- .select {
- float: top;
- z-index: 1;
- top: 0px;
- background: #191818;
- overflow-x: hidden;
- padding: 8px 10px;
- }
-
- .columnS {
- float: left;
- text-align: center;
- width: 50%;
- }
-
- .columnF {
- float: left;
- text-align: center;
- width: 33.33%;
- }
-
- .row:after {
- content: "";
- display: table;
- clear: both;
- }
+ .content {
+ margin: 0;
+ max-width: none;
+ }
- img {
- max-width: 100%;
- height: auto;
- }
+ .select {
+ float: top;
+ z-index: 1;
+ top: 0px;
+ background: #191818;
+ overflow-x: hidden;
+ padding: 8px 10px;
+ }
- @media (max-width: 1000px) {
.columnS {
- text-align: right;
- width: 100%;
+ float: left;
+ text-align: center;
+ width: 50%;
}
.columnF {
- width: 100%;
+ float: left;
+ text-align: center;
+ width: 33.33%;
+ }
+
+ .row:after {
+ content: "";
+ display: table;
+ clear: both;
}
- br {
- display: none;
+ img {
+ max-width: 100%;
+ height: auto;
+ }
+
+ @media (max-width: 1000px) {
+ .columnS {
+ text-align: right;
+ width: 100%;
+ }
+
+ .columnF {
+ width: 100%;
+ }
+
+ br {
+ display: none;
+ }
}
- }
</style>
<body>
- <div class="select">
- <div class="columnS ui-widget">
- <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
- <br>
- <input id="gene" size="19">
- </div>
- <div class="columnS">
- <label for="populations" style="font-size:18px;">
- <b>Select a group of cell populations:</b>
- </label>
- <br>
- <select name="populations" id="populations">
- <option selected="selected" value="Population"> Cell Populations</option>
- <option>Lineage</option>
- <option value="Zone">Prostatic Zone</option>
- <option>Patient</option>
- </select>
- </div>
- <br>
- <div style="text-align:center">
- <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
- </div>
- <hr>
- <div>
- <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
- <br>
- <span style="font-size:16px;">
- Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the
- prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and
- identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by
- population identity, cell lineage, patient, or dissected prostatic zone. This is the original sequencing depth
- published.
- </span>
- </div>
- </div>
- <div align="center">
- <h1 id="label.gene">NO GENE SELECTED</h1>
- <h2 id="label.populations"></h2>
- <div class="columnF">
- <h4 id="label.ClusterVis">
- </h3>
- <div class="img">
- <img id="img.ClusterVis" src="" />
+ <div class="select">
+ <div class="columnS ui-widget">
+ <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
+ <br>
+ <input id="gene" size="19">
</div>
- <br>
- </div>
- <div class="columnF">
- <h4 id="label.Feature">
- </h3>
- <div class="img">
- <img id="img.Feature" src="" />
+ <div class="columnS">
+ <label for="populations" style="font-size:18px;">
+ <b>Select a group of cell populations:</b>
+ </label>
+ <br>
+ <select name="populations" id="populations">
+ <option selected="selected" value="Population"> Cell Populations</option>
+ <option>Lineage</option>
+ <option value="Zone">Prostatic Zone</option>
+ <option>Patient</option>
+ </select>
</div>
<br>
+ <div style="text-align:center">
+ <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
+ </div>
+ <hr>
+ <div>
+ <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
+ <br>
+ <span style="font-size:16px;">
+ Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
+ the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
+ clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
+ be compared by population identity, cell lineage, patient, or dissected prostatic zone. This is the
+ original sequencing depth published.
+ </span>
+ </div>
</div>
- <div class="columnF">
- <h4 id="label.ViolinBox">
- </h3>
- <div class="img">
- <img id="img.ViolinBox" src="" />
+ <div align="center">
+ <h1 id="label.gene">NO GENE SELECTED</h1>
+ <h2 id="label.populations"></h2>
+ <div class="columnF">
+ <h4 id="label.ClusterVis">
+ </h3>
+ <div class="img">
+ <img id="img.ClusterVis" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.Feature">
+ </h3>
+ <div class="img">
+ <img id="img.Feature" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.ViolinBox">
+ </h3>
+ <div class="img">
+ <img id="img.ViolinBox" src="" />
+ </div>
+ <br>
</div>
- <br>
</div>
- </div>
- <hr>
- <div align="left">
- <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
- <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
- target="_blank">Cell Reports</a></span></div>
- <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
- <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
- target="_blank">GEO:
- GSE117403</a></span></div>
- <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
- W-R8CM</a></span></div>
- </div>
+ <hr>
+ <div align="left">
+ <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
+ <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
+ target="_blank">Cell Reports</a></span></div>
+ <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
+ <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
+ target="_blank">GEO:
+ GSE117403</a></span></div>
+ <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
+ W-R8CM</a></span></div>
+ </div>
</body>
{{ partial "footer.html" . }}
<head>
- <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
- <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
- <style>
- .ui-autocomplete {
- max-height: 200px;
- overflow-y: auto;
- overflow-x: hidden;
- }
- </style>
- <script>
- $(function () {
- $("#populations").selectmenu({ width: 230 });
- });
- $(function () {
- var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
- var selectedGene = $("#gene").autocomplete({
- source: genes.genes,
- maxResults: 10,
- maxShowItems: 10,
- minLength: 1,
- });
- });
- $("#analysis").click(function (event) {
- event.preventDefault();
- var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
- _gene = $("#gene").val().toUpperCase();
- if ($.inArray(_gene, genes.genes) < 0) {
- alert("Gene " + _gene + " not exist in the data.")
- return
- }
- document.getElementById("label.gene").innerHTML = _gene
- document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
- document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
- var img = document.getElementById("img.ClusterVis");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
- document.getElementById("label.Feature").innerHTML = "Feature Plot"
- var img = document.getElementById("img.Feature");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
- document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
- var img = document.getElementById("img.ViolinBox");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
- return (_gene)
- });
- </script>
+ <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+ <style>
+ .ui-autocomplete {
+ max-height: 200px;
+ overflow-y: auto;
+ overflow-x: hidden;
+ }
+ </style>
+ <script>
+ $(function () {
+ $("#populations").selectmenu({ width: 230 });
+ });
+ $(function () {
+ var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+ var selectedGene = $("#gene").autocomplete({
+ source: genes.genes,
+ maxResults: 10,
+ maxShowItems: 10,
+ minLength: 1,
+ });
+ });
+ $("#analysis").click(function (event) {
+ event.preventDefault();
+ var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+ _gene = $("#gene").val().toUpperCase();
+ if ($.inArray(_gene, genes.genes) < 0) {
+ alert("Gene " + _gene + " not exist in the data.")
+ return
+ }
+ document.getElementById("label.gene").innerHTML = _gene
+ document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
+ document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
+ var img = document.getElementById("img.ClusterVis");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
+ document.getElementById("label.Feature").innerHTML = "Feature Plot"
+ var img = document.getElementById("img.Feature");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
+ document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
+ var img = document.getElementById("img.ViolinBox");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
+ return (_gene)
+ });
+ </script>
</head>
\ No newline at end of file
diff --git a/layouts/custom/people.html b/layouts/custom/people.html
index 382df21..b867f93 100644
--- a/layouts/custom/people.html
+++ b/layouts/custom/people.html
@@ -10,18 +10,22 @@
.column {
float: left;
}
+
.left {
width: 25%;
}
+
.right {
width: 75%;
}
+
.row:after {
content: "";
display: table;
clear: both;
}
}
+
img.pic {
width: 175px;
padding: 7px;
diff --git a/layouts/custom/publications.html b/layouts/custom/publications.html
index 3fd85c1..90f9dfe 100644
--- a/layouts/custom/publications.html
+++ b/layouts/custom/publications.html
@@ -5,12 +5,15 @@
.column {
float: left;
}
+
.left {
width: 25%;
}
+
.right {
width: 75%;
}
+
.row:after {
content: "";
display: table;
@@ -26,35 +29,33 @@
<br>
<div>
{{ range first 10 (.Pages.ByParam "odate" ).Reverse }}
- <div class="row">
- <div class="column left">
- <img src="images/{{.Params.ppic}}" alt="" width="100px;"
- style="border:5px double black; border-radius:20%;">
- </div>
- <div class="column right">
- <h3>{{.Params.pname}}</h3>
- </div>
+ <div class="row">
+ <div class="column left">
+ <img src="images/{{.Params.ppic}}" alt="" width="100px;"
+ style="border:5px double black; border-radius:20%;">
+ </div>
+ <div class="column right">
+ <h3>{{.Params.pname}}</h3>
</div>
- {{ if not (eq .Params.ppubmed "") }}
- <h4><i><a
- href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}"
- target="_blank">
- {{else}}
- <h4><i><a href="{{.Params.plink}}">
- {{end}}
- {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
- {{ range first 1 .Params.prepo }}
- {{ if not (eq .title "") }}
+ </div>
+ {{ if not (eq .Params.ppubmed "") }}
+ <h4><i><a href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}" target="_blank">
+ {{else}}
+ <h4><i><a href="{{.Params.plink}}">
+ {{end}}
+ {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
+ {{ range first 1 .Params.prepo }}
+ {{ if not (eq .title "") }}
<u>Data Repository:</u><br>
- {{end}}
- {{end}}
- {{ range .Params.prepo }}
- {{ if not (eq .title "") }}
+ {{end}}
+ {{end}}
+ {{ range .Params.prepo }}
+ {{ if not (eq .title "") }}
<a href="{{.loc}}" target="_blank">{{.title}}</a><br>
- {{end}}
- {{end}}
- <hr><br>
- {{end}}
+ {{end}}
+ {{end}}
+ <hr><br>
+ {{end}}
</div>
</div>
diff --git a/layouts/custom/repository.html b/layouts/custom/repository.html
index 58b8c41..9686f8d 100644
--- a/layouts/custom/repository.html
+++ b/layouts/custom/repository.html
@@ -1,137 +1,978 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
-
<div class="content">
- {{ .Content }}
-
-
- <!-- Sidebar for Filters -->
-
- <div class= "sidenav">
- <button class="dropdown-btn">
- Type 2 Diabetes
- <i class="fa fa-caret-down"></i>
- </button>
-
- <div id="filter">
- <input type="checkbox" name="Type 2 diabetes" value="1"> T2 Diabetes <span class="numbers" id="Type2diabetes1">#</span></input>
-
- <br>
- <input type="checkbox" name="Type 2 diabetes" value="0"> No T2 Diabetes </input>
- <p class = "numbers" id="Type2diabetes0">#</p>
- </div>
-
- <button class="dropdown-btn">
- Age
- <i class="fa fa-caret-down"></i>
- </button>
-
- <div id="filter">
- <input value= "Enter Age Here"></input>
-
- </div>
-
- <p id="displayFiles">0</p>
-
-
+ {{ .Content }}
</div>
+<style>
+ .pure-menu-heading {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
+ .pure-menu {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
- <!-- Summary of Filtered Data -->
- <div id="summary">
- </div>
-
- <!-- Files of Filtered Data -->
- <div id="patientFiles">
- </div>
-
-
-</div>
-
+ .pure-menu-social {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
-<head>
- <link rel="stylesheet" type="text/css" href="/css/sidenavRepository.css"/>
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
- <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
- <script src="/js/repositoryJS.js"></script>
-</head>
+ .small-print {
+ color: #777;
+ font-family: sans-serif;
+ }
-<body>
-<script>
-/*$(document).ready(function(){
-
-//declare global vars
- var results = []; //array of records that match the filters
- var data = {{ index .Site.Data.scRNAseq_huPr_D.updated_cleaned_json }};
- var numbers = $("#filter").find(".numbers"); //array of all the places we want to update with the # of records that match the filters
- var filters = [];
-
-//filtering function
- $("input").click(function(){
-
- // get specific vars
- var name = $(this).attr("name");
- var value = $(this).attr("value");
- var id = name + value;
- id= id.replace(/\s+/g, '');
-
-// if checkbox is checked: add filter values to filter
- if ($(this).prop("checked") == true){
-
- var i;
- for (i =0; i < data.length; i++){
- if( data[i][name] == value){
- results.push(data[i]);
- $("#"+id).text[numbers.length];
- }
- }
- }
-
-//if checkbox is not checked: remove filter values from filter
- else if ($(this).prop("checked") == false){
- var i;
- for (i=0; i<results.length; i++){
- if (results[i][name]== value){
- results.splice(i, 1);
- i--;
+ .content {
+ margin: 0;
+ max-width: none;
}
- }
-
- }
-
-//check data to pull all records that match the current filters
- var i;
- var j;
- for (i = 0; i<numbers.length; i++){
- var count = 0;
- $('#displayFiles').text(numbers.length);
-
- for (j=0; j <results.length; j++){
- var id2 = results[j][name]. + results[j][name];
- // id2 = id2.replace(/\s+/g, '');
- // $('#displayFiles').text(id2);
- if (id2 == numbers[i][id]){
- count++;
- $('#displayFiles').text(count);
- }
- }
- }
- });
-});
-*/
-</script>
-</body>
+ .select {
+ float: top;
+ z-index: 1;
+ top: 0px;
+ color: #777;
+ background: #191818;
+ overflow-x: hidden;
+ padding: 8px 10px;
+ }
+ .panel_canvas {
+ width: 175px;
+ }
+ .icon {
+ font-size: 50px;
+ padding: 5px;
+ }
+ th,
+ td {
+ padding: 5px 15px;
+ text-align: center;
+ }
+ .no_checkbox>i.jstree-checkbox {
+ display: none
+ }
+</style>
+<head>
+ <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
+ <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"></script>
+ <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css">
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/jstree.min.js"></script>
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.5.0/Chart.min.js"></script>
+ <script>
+ $(function () {
+ var repo = {{ index .Site.Data.repository.repository }}
+ var filters = {{ index .Site.Data.repository.filters }}
+ $("#jstree").jstree({
+ "core": {
+ "data": filters,
+ "themes": {
+ "theme": "default",
+ "dots": false,
+ "icons": false
+ },
+ },
+ "checkbox": {
+ "keep_selected_style": false,
+ cascade: "",
+ three_state: false,
+ whole_node: false,
+ tie_selection: false
+ },
+ "plugins": ["themes", "checkbox"]
+ })
+
+ $("#jstree").bind("check_node.jstree uncheck_node.jstree", function (e, data) {
+ var checked = $("#jstree").jstree("get_checked")
+ var filter = []
+ for (i = 0; i < checked.length; i++) {
+ for (j = 0; j < filters.length; j++) {
+ if (checked[i] == filters[j].id) {
+ filter.push(filters[j].text)
+ }
+ }
+ }
+ filtered = filterRepo(repo, checked)
+ filterRepoGroups_out = filterRepoGroups(repo, filtered)
+ filtered_dis = filterRepoGroups_out[0]
+ filtered_bmi = filterRepoGroups_out[1]
+ filtered_t2d = filterRepoGroups_out[2]
+ filtered_eth = filterRepoGroups_out[3]
+ filtered_age = filterRepoGroups_out[4]
+ filtered_prv = filterRepoGroups_out[5]
+ filtered_psa = filterRepoGroups_out[6]
+ filtered_ari = filterRepoGroups_out[7]
+ filtered_alb = filterRepoGroups_out[8]
+ document.getElementById("total").innerHTML = filtered.length
+ if (checked.length == 0) {
+ document.getElementById("filters").innerHTML = "NO"
+ } else {
+ document.getElementById("filters").innerHTML = filter
+ }
+ filterDoughnut_out = filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa, filtered_ari, filtered_alb)
+ doughnut_data_dis = filterDoughnut_out[0]
+ doughnut_data_bmi = filterDoughnut_out[1]
+ doughnut_data_t2d = filterDoughnut_out[2]
+ doughnut_data_eth = filterDoughnut_out[3]
+ doughnut_data_age = filterDoughnut_out[4]
+ doughnut_data_prv = filterDoughnut_out[5]
+ doughnut_data_psa = filterDoughnut_out[6]
+ doughnut_data_ari = filterDoughnut_out[7]
+ doughnut_data_alb = filterDoughnut_out[8]
+ dis.destroy()
+ dis = new Chart(document.getElementById("doughnut-dis"), { type: "doughnut", data: doughnut_data_dis, options: doughnut_options })
+ bmi.destroy()
+ bmi = new Chart(document.getElementById("doughnut-bmi"), { type: "doughnut", data: doughnut_data_bmi, options: doughnut_options })
+ t2d.destroy()
+ t2d = new Chart(document.getElementById("doughnut-t2d"), { type: "doughnut", data: doughnut_data_t2d, options: doughnut_options })
+ eth.destroy()
+ eth = new Chart(document.getElementById("doughnut-eth"), { type: "doughnut", data: doughnut_data_eth, options: doughnut_options })
+ age.destroy()
+ age = new Chart(document.getElementById("doughnut-age"), { type: "doughnut", data: doughnut_data_age, options: doughnut_options })
+ prv.destroy()
+ prv = new Chart(document.getElementById("doughnut-prv"), { type: "doughnut", data: doughnut_data_prv, options: doughnut_options })
+ psa.destroy()
+ psa = new Chart(document.getElementById("doughnut-psa"), { type: "doughnut", data: doughnut_data_psa, options: doughnut_options })
+ ari.destroy()
+ ari = new Chart(document.getElementById("doughnut-ari"), { type: "doughnut", data: doughnut_data_ari, options: doughnut_options })
+ alb.destroy()
+ alb = new Chart(document.getElementById("doughnut-alb"), { type: "doughnut", data: doughnut_data_alb, options: doughnut_options })
+ tableData(repo, filtered)
+ })
+ checked = []
+ filtered = filterRepo(repo, checked)
+ filterRepoGroups_out = filterRepoGroups(repo, filtered)
+ filtered_dis = filterRepoGroups_out[0]
+ filtered_bmi = filterRepoGroups_out[1]
+ filtered_t2d = filterRepoGroups_out[2]
+ filtered_eth = filterRepoGroups_out[3]
+ filtered_age = filterRepoGroups_out[4]
+ filtered_prv = filterRepoGroups_out[5]
+ filtered_psa = filterRepoGroups_out[6]
+ filtered_ari = filterRepoGroups_out[7]
+ filtered_alb = filterRepoGroups_out[8]
+ document.getElementById("total").innerHTML = filtered.length
+ document.getElementById("filters").innerHTML = "NO"
+ filterDoughnut_out = filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa, filtered_ari, filtered_alb)
+ doughnut_data_dis = filterDoughnut_out[0]
+ doughnut_data_bmi = filterDoughnut_out[1]
+ doughnut_data_t2d = filterDoughnut_out[2]
+ doughnut_data_eth = filterDoughnut_out[3]
+ doughnut_data_age = filterDoughnut_out[4]
+ doughnut_data_prv = filterDoughnut_out[5]
+ doughnut_data_psa = filterDoughnut_out[6]
+ doughnut_data_ari = filterDoughnut_out[7]
+ doughnut_data_alb = filterDoughnut_out[8]
+ dis = new Chart(document.getElementById("doughnut-dis"), { type: "doughnut", data: doughnut_data_dis, options: doughnut_options })
+ bmi = new Chart(document.getElementById("doughnut-bmi"), { type: "doughnut", data: doughnut_data_bmi, options: doughnut_options })
+ t2d = new Chart(document.getElementById("doughnut-t2d"), { type: "doughnut", data: doughnut_data_t2d, options: doughnut_options })
+ eth = new Chart(document.getElementById("doughnut-eth"), { type: "doughnut", data: doughnut_data_eth, options: doughnut_options })
+ age = new Chart(document.getElementById("doughnut-age"), { type: "doughnut", data: doughnut_data_age, options: doughnut_options })
+ prv = new Chart(document.getElementById("doughnut-prv"), { type: "doughnut", data: doughnut_data_prv, options: doughnut_options })
+ psa = new Chart(document.getElementById("doughnut-psa"), { type: "doughnut", data: doughnut_data_psa, options: doughnut_options })
+ ari = new Chart(document.getElementById("doughnut-ari"), { type: "doughnut", data: doughnut_data_ari, options: doughnut_options })
+ alb = new Chart(document.getElementById("doughnut-alb"), { type: "doughnut", data: doughnut_data_alb, options: doughnut_options })
+
+ tableData(repo, filtered)
+ })
+ var doughnut_options = {
+ responsive: true,
+ legend: {
+ display: false
+ }
+ }
+ function filterRepo(repo, checked) {
+ filtered = []
+ filtered_dis = []
+ filtered_eth = []
+ filtered_age = []
+ filtered_bmi = []
+ filtered_t2d = []
+ filtered_bphsurg = []
+ filtered_ari = []
+ filtered_aril = []
+ filtered_prvol = []
+ filtered_repo_pr_cry = []
+ filtered_repo_pr_ff = []
+ filtered_repo_pr_ffpe = []
+ filtered_repo_pr_oct = []
+ filtered_repo_bl = []
+ filtered_repo_sv = []
+ filtered_repo_vd = []
+ filtered_repo_ut = []
+ for (i = 0; i < repo.length; i++) {
+ filtered.push(repo[i].PatientID)
+ if (checked.includes("disease.d")) {
+ if (repo[i]["Disease Status"] == "Donor") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("disease.b")) {
+ if (repo[i]["Disease Status"] == "BPH") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("disease.c")) {
+ if (repo[i]["Disease Status"] == "Cancer") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("disease.d") && !checked.includes("disease.b") && !checked.includes("disease.c")) {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ if (checked.includes("ethn.aa")) {
+ if (repo[i].Ethnicity == "AA") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.as")) {
+ if (repo[i].Ethnicity == "Asian") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.ca")) {
+ if (repo[i].Ethnicity == "Cauc") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.hi")) {
+ if (repo[i].Ethnicity == "Hisp") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.uk")) {
+ if (repo[i].Ethnicity == "unknown") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("ethn.aa") && !checked.includes("ethn.as") && !checked.includes("ethn.ca") && !checked.includes("ethn.hi") && !checked.includes("ethn.uk")) {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ if (checked.includes("age.40")) {
+ if (repo[i].Age < 41) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.50")) {
+ if (repo[i].Age >= 41 && repo[i].Age < 51) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.60")) {
+ if (repo[i].Age >= 51 && repo[i].Age < 61) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.70")) {
+ if (repo[i].Age >= 61 && repo[i].Age < 71) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.80")) {
+ if (repo[i].Age >= 71 && repo[i].Age < 81) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.90")) {
+ if (repo[i].Age >= 81 && repo[i].Age < 91) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.100")) {
+ if (repo[i].Age >= 91) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.uk")) {
+ if (repo[i].Age == "unknown") {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("age.40") && !checked.includes("age.50") && !checked.includes("age.60") && !checked.includes("age.70") && !checked.includes("age.80") && !checked.includes("age.90") && !checked.includes("age.100") && !checked.includes("age.uk")) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ if (checked.includes("bmi.uw")) {
+ if (repo[i].BMI < 18.5) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.nw")) {
+ if (repo[i].BMI >= 18.5 && repo[i].BMI < 25) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.ow")) {
+ if (repo[i].BMI >= 25 && repo[i].BMI < 30) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.ob")) {
+ if (repo[i].BMI >= 30 && repo[i].BMI < 35) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.vo")) {
+ if (repo[i].BMI >= 35 && repo[i].BMI < 40) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.so")) {
+ if (repo[i].BMI >= 40) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.uk")) {
+ if (repo[i].BMI == "unknown") {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("bmi.uw") && !checked.includes("bmi.nw") && !checked.includes("bmi.ow") && !checked.includes("bmi.ob") && !checked.includes("bmi.vo") && !checked.includes("bmi.so") && !checked.includes("bmi.uk")) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ if (checked.includes("t2d.y")) {
+ if (repo[i]["Type 2 diabetes"] == 1) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("t2d.n")) {
+ if (repo[i]["Type 2 diabetes"] == 0) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("t2d.uk")) {
+ if (repo[i]["Type 2 diabetes"] == "unknown") {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("t2d.y") && !checked.includes("t2d.n") && !checked.includes("t2d.uk")) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ if (checked.includes("bphsurg.simp")) {
+ if (repo[i]["BPH surgery"] == "Simple") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bphsurg.turp")) {
+ if (repo[i]["BPH surgery"] == "TURP") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bphsurg.uk")) {
+ if (repo[i]["BPH surgery"] == "unknown") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("bphsurg.simp") && !checked.includes("bphsurg.turp") && !checked.includes("bphsurg.uk")) {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ if (checked.includes("5ari.y")) {
+ if (repo[i]["5ARI"] == 1) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5ari.n")) {
+ if (repo[i]["5ARI"] == 0) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5ari.uk")) {
+ if (repo[i]["5ARI"] == "unknown") {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("5ari.y") && !checked.includes("5ari.n") && !checked.includes("5ari.uk")) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ if (checked.includes("5aril.10")) {
+ if (repo[i]["5ARI length (months)"] < 10) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.20")) {
+ if (repo[i]["5ARI length (months)"] >= 10 && repo[i]["5ARI length (months)"] < 20) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.30")) {
+ if (repo[i]["5ARI length (months)"] >= 20) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.uk")) {
+ if (repo[i]["5ARI length (months)"] == "unknown") {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.na")) {
+ if (repo[i]["5ARI length (months)"] == "na") {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("5aril.10") && !checked.includes("5aril.20") && !checked.includes("5aril.30") && !checked.includes("5aril.uk") && !checked.includes("5aril.na")) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ if (checked.includes("prvol.low")) {
+ if (repo[i]["Prostate volume"] < 31) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.med")) {
+ if (repo[i]["Prostate volume"] >= 31 && repo[i]["Prostate volume"] < 81) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.hi")) {
+ if (repo[i]["Prostate volume"] >= 81 && repo[i]["Prostate volume"] < 121) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.vhi")) {
+ if (repo[i]["Prostate volume"] >= 121) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.uk")) {
+ if (repo[i]["Prostate volume"] == "unknown") {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("prvol.low") && !checked.includes("prvol.med") && !checked.includes("prvol.hi") && !checked.includes("prvol.vhi") && !checked.includes("prvol.uk")) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.cry")) {
+ if (repo[i]["Cryopreserved single cells"] == 1) {
+ filtered_repo_pr_cry.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_cry.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.ff")) {
+ if (repo[i]["Flash frozen"] == 1) {
+ filtered_repo_pr_ff.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_ff.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.ffpe")) {
+ if (repo[i]["Paraffin block"] == 1) {
+ filtered_repo_pr_ffpe.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_ffpe.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.oct")) {
+ if (repo[i]["OCT block"] == 1) {
+ filtered_repo_pr_oct.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_oct.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.bl")) {
+ if (repo[i]["Matching bladder"] == 1) {
+ filtered_repo_bl.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_bl.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.sv")) {
+ if (repo[i]["Matching Seminal vesicle"] == 1) {
+ filtered_repo_sv.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_sv.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.vd")) {
+ if (repo[i]["Matching vas deferens"] == 1) {
+ filtered_repo_vd.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_vd.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.ut")) {
+ if (repo[i]["Matching ureter"] == 1) {
+ filtered_repo_ut.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_ut.push(repo[i].PatientID)
+ }
+ }
+ filtered = intersect(filtered, filtered_dis)
+ filtered = intersect(filtered, filtered_eth)
+ filtered = intersect(filtered, filtered_age)
+ filtered = intersect(filtered, filtered_bmi)
+ filtered = intersect(filtered, filtered_t2d)
+ filtered = intersect(filtered, filtered_bphsurg)
+ filtered = intersect(filtered, filtered_ari)
+ filtered = intersect(filtered, filtered_aril)
+ filtered = intersect(filtered, filtered_prvol)
+ filtered = intersect(filtered, filtered_repo_pr_cry)
+ filtered = intersect(filtered, filtered_repo_pr_ff)
+ filtered = intersect(filtered, filtered_repo_pr_ffpe)
+ filtered = intersect(filtered, filtered_repo_pr_oct)
+ filtered = intersect(filtered, filtered_repo_bl)
+ filtered = intersect(filtered, filtered_repo_sv)
+ filtered = intersect(filtered, filtered_repo_vd)
+ filtered = intersect(filtered, filtered_repo_ut)
+
+ filtered = filtered.filter(onlyUnique)
+ if (checked.length == 0) {
+ filtered = []
+ for (i = 0; i < repo.length; i++) {
+ filtered.push(repo[i].PatientID)
+ }
+ }
+
+ document.getElementById("test").innerHTML = ""
+
+ return filtered
+ }
+ function filterRepoGroups(repo, filtered) {
+ filtered_dis = []
+ filtered_dis_d = []
+ filtered_dis_b = []
+ filtered_dis_c = []
+ filtered_bmi = []
+ filtered_bmi_uw = []
+ filtered_bmi_nw = []
+ filtered_bmi_ow = []
+ filtered_bmi_ob = []
+ filtered_bmi_vo = []
+ filtered_bmi_so = []
+ filtered_bmi_uk = []
+ filtered_t2d = []
+ filtered_t2d_no = []
+ filtered_t2d_ys = []
+ filtered_t2d_uk = []
+ filtered_eth = []
+ filtered_eth_aa = []
+ filtered_eth_as = []
+ filtered_eth_ca = []
+ filtered_eth_hi = []
+ filtered_eth_uk = []
+ filtered_eth = []
+ filtered_eth_aa = []
+ filtered_eth_as = []
+ filtered_eth_ca = []
+ filtered_eth_hi = []
+ filtered_eth_uk = []
+ filtered_age = []
+ filtered_age_40 = []
+ filtered_age_50 = []
+ filtered_age_60 = []
+ filtered_age_70 = []
+ filtered_age_80 = []
+ filtered_age_90 = []
+ filtered_age_100 = []
+ filtered_age_uk = []
+ filtered_prv = []
+ filtered_prv_40 = []
+ filtered_prv_50 = []
+ filtered_prv_60 = []
+ filtered_prv_uk = []
+ filtered_psa = []
+ filtered_psa_nm = []
+ filtered_psa_lr = []
+ filtered_psa_hr = []
+ filtered_psa_uk = []
+ filtered_ari = []
+ filtered_ari_ys = []
+ filtered_ari_no = []
+ filtered_ari_uk = []
+ filtered_alb = []
+ filtered_alb_ys = []
+ filtered_alb_no = []
+ filtered_alb_uk = []
+ for (i = 0; i < repo.length; i++) {
+ if (filtered.includes(repo[i].PatientID)) {
+ if (repo[i]["Disease Status"] == "Donor") {
+ filtered_dis_d.push(repo[i].PatientID)
+ }
+ if (repo[i]["Disease Status"] == "BPH") {
+ filtered_dis_b.push(repo[i].PatientID)
+ }
+ if (repo[i]["Disease Status"] == "Cancer") {
+ filtered_dis_c.push(repo[i].PatientID)
+ }
+
+ if (repo[i].BMI < 18.5) {
+ filtered_bmi_uw.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 18.5 && repo[i].BMI < 25) {
+ filtered_bmi_nw.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 25 && repo[i].BMI < 30) {
+ filtered_bmi_ow.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 30 && repo[i].BMI < 35) {
+ filtered_bmi_ob.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 35 && repo[i].BMI < 40) {
+ filtered_bmi_vo.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 40) {
+ filtered_bmi_so.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI == "unknown") {
+ filtered_bmi_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["Type 2 diabetes"] == 0) {
+ filtered_t2d_no.push(repo[i].PatientID)
+ }
+ if (repo[i]["Type 2 diabetes"] == 1) {
+ filtered_t2d_ys.push(repo[i].PatientID)
+ }
+ if (repo[i]["Type 2 diabetes"] == "unknown") {
+ filtered_t2d_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].Ethnicity == "AA") {
+ filtered_eth_aa.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Asian") {
+ filtered_eth_as.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Cauc") {
+ filtered_eth_ca.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Hisp") {
+ filtered_eth_hi.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "unknown") {
+ filtered_eth_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].Age < 41) {
+ filtered_age_40.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 41 && repo[i].Age < 51) {
+ filtered_age_50.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 51 && repo[i].Age < 61) {
+ filtered_age_60.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 61 && repo[i].Age < 71) {
+ filtered_age_70.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 71 && repo[i].Age < 81) {
+ filtered_age_80.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 81 && repo[i].Age < 91) {
+ filtered_age_90.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 91) {
+ filtered_age_100.push(repo[i].PatientID)
+ }
+ if (repo[i].Age == "unknown") {
+ filtered_age_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["Prostate volume"] < 41) {
+ filtered_prv_40.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] >= 41 && repo[i]["Prostate volume"] < 51) {
+ filtered_prv_50.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] >= 51) {
+ filtered_prv_60.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] == "unknown") {
+ filtered_prv_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].PSA < 1) {
+ filtered_psa_nm.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA >= 1 && repo[i].PSA < 3) {
+ filtered_psa_lr.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA >= 3) {
+ filtered_psa_hr.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA == "unknown") {
+ filtered_psa_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["5ARI"] == 1) {
+ filtered_ari_ys.push(repo[i].PatientID)
+ }
+ if (repo[i]["5ARI"] == 0) {
+ filtered_ari_no.push(repo[i].PatientID)
+ }
+ if (repo[i]["5ARI"] == "unknown") {
+ filtered_ari_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["Alpha blocker"] == 1) {
+ filtered_alb_ys.push(repo[i].PatientID)
+ }
+ if (repo[i]["Alpha blocker"] == 0) {
+ filtered_alb_no.push(repo[i].PatientID)
+ }
+ if (repo[i]["Alpha blocker"] == "unknown") {
+ filtered_alb_uk.push(repo[i].PatientID)
+ }
+ }
+ }
+ filtered_dis = [filtered_dis_d.length, filtered_dis_b.length, filtered_dis_c.length]
+ filtered_bmi = [filtered_bmi_uw.length, filtered_bmi_nw.length, filtered_bmi_ow.length, filtered_bmi_ob.length, filtered_bmi_vo.length, filtered_bmi_so.length, filtered_bmi_uk.length]
+ filtered_t2d = [filtered_t2d_no.length, filtered_t2d_ys.length, filtered_t2d_uk.length]
+ filtered_eth = [filtered_eth_aa.length, filtered_eth_as.length, filtered_eth_ca.length, filtered_eth_hi.length, filtered_eth_uk.length]
+ filtered_age = [filtered_age_40.length, filtered_age_50.length, filtered_age_60.length, filtered_age_70.length, filtered_age_80.length, filtered_age_90.length, filtered_age_100.length, filtered_age_uk.length]
+ filtered_prv = [filtered_prv_40.length, filtered_prv_50.length, filtered_prv_60.length, filtered_prv_uk.length]
+ filtered_psa = [filtered_psa_nm.length, filtered_psa_lr.length, filtered_psa_hr.length, filtered_psa_uk.length]
+ filtered_ari = [filtered_ari_ys.length, filtered_ari_no.length, filtered_ari_uk.length]
+ filtered_alb = [filtered_alb_ys.length, filtered_alb_no.length, filtered_alb_uk.length]
+
+ return [
+ filtered_dis,
+ filtered_bmi,
+ filtered_t2d,
+ filtered_eth,
+ filtered_age,
+ filtered_prv,
+ filtered_psa,
+ filtered_ari,
+ filtered_alb
+ ]
+ }
+ function filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa, filtered_ari, filtered_alb) {
+ doughnut_data_dis = []
+ doughnut_data_bmi = []
+ doughnut_data_t2d = []
+ doughnut_data_eth = []
+ doughnut_data_age = []
+ doughnut_data_prv = []
+ doughnut_data_psa = []
+ doughnut_data_ari = []
+ doughnut_data_alb = []
+ doughnut_data_dis = {
+ labels: ["Donor (normal)", "BPH", "Prostate Cancer"],
+ datasets: [{
+ data: filtered_dis,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+ doughnut_data_bmi = {
+ labels: ["Underweight", "Normal Weight", "Overweight", "Obese", "Very Obese", "Severely Obese", "Unknown"],
+ datasets: [{
+ data: filtered_bmi,
+ backgroundColor: ["#440154", "#443A83", "#31688E", "#21908C", "#35B779", "#8FD744", "#FDE725"]
+ }]
+ }
+ doughnut_data_t2d = {
+ labels: ["No", "Yes", "Unknown"],
+ datasets: [{
+ data: filtered_t2d,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+ doughnut_data_eth = {
+ labels: ["African American", "Asian", "Caucasian", "Hispanic", "Unknown"],
+ datasets: [{
+ data: filtered_eth,
+ backgroundColor: ["#440154", "#3B528B", "#21908C", "#5DC863", "#FDE725"]
+ }]
+ }
+ doughnut_data_age = {
+ labels: ["0-40yo", "41-50yo", "51-60yo", "61-70yo", "71-80yo", "81-90yo", "91+yo", "Unknown"],
+ datasets: [{
+ data: filtered_age,
+ backgroundColor: ["#440154", "#46337E", "#365C8D", "#277F8E", "#1FA187", "#4AC16D", "#9FDA3A", "#FDE725"]
+ }]
+ }
+ doughnut_data_prv = {
+ labels: ["0-40cc", "41-50cc", "50+cc", "Unknown"],
+ datasets: [{
+ data: filtered_prv,
+ backgroundColor: ["#440154", "#31688E", "#35B779", "#FDE725"]
+ }]
+ }
+ doughnut_data_psa = {
+ labels: ["Normal", "Low Risk", "High Risk", "Unknown"],
+ datasets: [{
+ data: filtered_psa,
+ backgroundColor: ["#440154", "#31688E", "#35B779", "#FDE725"]
+ }]
+ }
+ doughnut_data_ari = {
+ labels: ["Yes", "No", "Unknown"],
+ datasets: [{
+ data: filtered_ari,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+ doughnut_data_alb = {
+ labels: ["Yes", "No", "Unknown"],
+ datasets: [{
+ data: filtered_alb,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+
+ return [
+ doughnut_data_dis,
+ doughnut_data_bmi,
+ doughnut_data_t2d,
+ doughnut_data_eth,
+ doughnut_data_age,
+ doughnut_data_prv,
+ doughnut_data_psa,
+ doughnut_data_ari,
+ doughnut_data_alb
+ ]
+ }
+ function tableData(repo, fitered) {
+ let table = document.getElementById("samplesTable")
+ while (table.rows.length > 1) {
+ table.deleteRow(-1);
+ }
+ for (i = 0; i < repo.length; i++) {
+ if (filtered.includes(repo[i].PatientID)) {
+ let newRow = table.insertRow(-1)
+ var row_ds = newRow.insertCell(0)
+ var row_si = newRow.insertCell(1)
+ var row_ag = newRow.insertCell(2)
+ var row_et = newRow.insertCell(3)
+ row_ds.innerHTML = repo[i]["Disease Status"]
+ row_si.innerHTML = repo[i]["Study ID"]
+ row_ag.innerHTML = repo[i].Age
+ row_et.innerHTML = repo[i].Ethnicity
+ }
+ }
+ }
+ function onlyUnique(value, index, self) {
+ return self.indexOf(value) === index
+ }
+ function intersect(a, b) {
+ var t;
+ if (b.length > a.length) t = b, b = a, a = t;
+ return a.filter(function (e) {
+ return b.indexOf(e) > -1;
+ });
+ }
+ </script>
+</head>
+<body>
+ <div class="select">
+ <div id="jstree"></div>
+ </div>
+ <br>
+ <div class="container" style="max-width: none;">
+ <div class="row">
+ <div class="col-8" style="color: grey; background-color: #191818;">
+ <h4 id="total"></h4>
+ <h5>Patients</h5>
+ </div>
+ <div class="col-4 text-right" style="color: grey; background-color: #191818;">
+ <i class='fa fa-user icon'></i>
+ </div>
+ </div>
+ <div class="row">
+ <div class="col-8" style="color: grey; background-color: #191818;">
+ <h4 id="filters"></h4>
+ <h5>Filters</h5>
+ </div>
+ <div class="col-4 text-right" style="color: grey; background-color: #191818;">
+ <i class='fa fa-filter icon'></i>
+ </div>
+ </div>
+ </div>
+ <p id="test">Test</p>
+ <hr>
+ <div class="container" align=center style="max-width: none;">
+ <div class="row">
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Disease Status</p>
+ <hr>
+ <canvas id="doughnut-dis" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>BMI</p>
+ <hr>
+ <canvas id="doughnut-bmi" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Type 2 Diabetes</p>
+ <hr>
+ <canvas id="doughnut-t2d" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Ethnicity</p>
+ <hr>
+ <canvas id="doughnut-eth" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Age</p>
+ <hr>
+ <canvas id="doughnut-age" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Prostate Volume</p>
+ <hr>
+ <canvas id="doughnut-prv" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>PSA</p>
+ <hr>
+ <canvas id="doughnut-psa" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>5ARI Treatment</p>
+ <hr>
+ <canvas id="doughnut-ari" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Alpha Blocker Treatment</p>
+ <hr>
+ <canvas id="doughnut-alb" width="150" height="150"></canvas>
+ </div>
+ </div>
+ </div>
+ </div>
+ <hr>
+ <div class="container" align=center style="max-width: none;">
+ <table id="samplesTable" border="1">
+ <tr>
+ <th>Disease</th>
+ <th>ID</th>
+ <th>Age</th>
+ <th>Ethnicity</th>
+ </tr>
+ </table>
+ </div>
+</body>
{{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/layouts/custom/research.html b/layouts/custom/research.html
index e1c9ca3..d2dc31d 100644
--- a/layouts/custom/research.html
+++ b/layouts/custom/research.html
@@ -11,28 +11,33 @@
display: table;
clear: both;
}
+
div.fig {
padding: 1px;
border: 1px solid black;
margin: auto;
background-color: LightGrey;
}
+
div.fig img {
width: 500px;
max-width: 100%;
height: auto;
padding: 1px;
}
+
div.lab {
text-align: justify;
padding-left: 10px;
padding-right: 10px;
}
+
@media (min-width: 1000px) {
div.fig {
float: left;
margin: 1px 10px 1px 1px;
}
+
br {
display: none;
}
@@ -42,41 +47,30 @@
<div class="section">
<H1 align="center">Overview</H1>
<p style="text-align:justify; font-size:18px">
- The main goals of the Strand lab are to create accurate cellular
- atlases of the human and mouse lower
- urinary tract, characterize the molecular and cellular alterations
- in human lower urinary tract disease, and
+ The main goals of the Strand lab are to create accurate cellular atlases of the human and mouse lower
+ urinary tract, characterize the molecular and cellular alterations in human lower urinary tract disease, and
build appropriate models of the human disease in novel mouse models.
</p>
</div>
<div class="section">
<H1 align="center">Benign Prostatic Hyperplasia</H1>
<div class="fig" style="max-width:250px">
- <img src="/research.images/prostate.jpg" alt="prostate" class="img"
- />
+ <img src="/research.images/prostate.jpg" alt="prostate" class="img" />
<div class="lab">
- <p>Cross-section of a prostate gland, showing the transition
- zone (TZ) and the peripheral zone (PZ)</p>
+ <p>Cross-section of a prostate gland, showing the transition zone (TZ) and the peripheral zone (PZ)</p>
</div>
<p class="br"></p>
</div>
<p style="text-align:justify; font-size:18px">
- A goal of the Strand laboratory is to understand the cellular and
- molecular biology of lower urinary tract
- symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder
- dysfunction. BPH/LUTS is present in the
- vast majority of men over 70 years old resulting in medical
- treatment or surgical intervention.
+ A goal of the Strand laboratory is to understand the cellular and molecular biology of lower urinary tract
+ symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder dysfunction. BPH/LUTS is present in the
+ vast majority of men over 70 years old resulting in medical treatment or surgical intervention.
</p>
<p style="text-align:justify; font-size:18px">
- We focus on translational questions related to progression of
- BPH/LUTS in order to develop new targets for
- therapeutic intervention. In particular, we are interested in
- characterizing the cellular composition of
- particular phenotypes that are resistant to current therapies. We
- use a combination of single cell RNA
- sequencing, flow cytometry and immunohistochemistry on normal and
- diseased human specimens to build a
+ We focus on translational questions related to progression of BPH/LUTS in order to develop new targets for
+ therapeutic intervention. In particular, we are interested in characterizing the cellular composition of
+ particular phenotypes that are resistant to current therapies. We use a combination of single cell RNA
+ sequencing, flow cytometry and immunohistochemistry on normal and diseased human specimens to build a
cellular atlas of prostate and bladder disease.
</p>
</div>
@@ -84,82 +78,56 @@
<div class="section">
<H1 align="center">Pathological Heterogeneity in BPH</H1>
<div class="fig" style="max-width:500px">
- <img src="/research.images/pheno.jpg" alt="phenotypes" class="img"
- />
+ <img src="/research.images/pheno.jpg" alt="phenotypes" class="img" />
<div class="lab">
- <p>Phenotypic diversity in BPH. Left: glandular enlargement.
- Middle: Stromal enlargement. Right: Mixed
+ <p>Phenotypic diversity in BPH. Left: glandular enlargement. Middle: Stromal enlargement. Right: Mixed
type.</p>
</div>
</div>
<p style="text-align:justify; font-size:18px">
- We believe that the basis for heterogeneous clinical responses in
- BPH is pathologic diversity. There are a
- number of phenotypes evident across and even within patients. In one
- area, a patient can display a stromal
+ We believe that the basis for heterogeneous clinical responses in BPH is pathologic diversity. There are a
+ number of phenotypes evident across and even within patients. In one area, a patient can display a stromal
tumor while the other area display an epithelial nodule.
</p>
<p style="text-align:justify; font-size:18px">
- Our goal is to provide a rational basis for therapeutically treating
- these individual phenotypes by
- dissecting them macroscopically and then comparing their
- cell-specific molecular profiles to reduce the
- noise of cellular heterogeneity and inflammation. Our first goal is
- to identify a cell or cells of origin
- for the varying phenotypes by phenotyping the tissues with single
- cell RNA sequencing. This includes a
- comprehensive evaluation of the immune and inflammatory infiltrate
- as well as fluctuations in epithelial and
+ Our goal is to provide a rational basis for therapeutically treating these individual phenotypes by
+ dissecting them macroscopically and then comparing their cell-specific molecular profiles to reduce the
+ noise of cellular heterogeneity and inflammation. Our first goal is to identify a cell or cells of origin
+ for the varying phenotypes by phenotyping the tissues with single cell RNA sequencing. This includes a
+ comprehensive evaluation of the immune and inflammatory infiltrate as well as fluctuations in epithelial and
stromal subpopulations.
</p>
<p style="text-align:justify; font-size:18px">
- We are subsequently isolating the cell types of interest and
- performing molecular profiling. Based on these
- targets, we will use our mouse and cell culture models to
- experimentally test our hypotheses.
+ We are subsequently isolating the cell types of interest and performing molecular profiling. Based on these
+ targets, we will use our mouse and cell culture models to experimentally test our hypotheses.
</p>
</div>
<div class="section">
<H1 align="center">Clinical Heterogeneity in BPH</H1>
<p style="text-align:justify; font-size:18px">
- It is clear from clinical trials of medications for BPH that
- personalized therapies will be needed due to
- the highly variable responses. Typically, patients complaining of
- lower urinary tract symptoms are placed on
- an alpha-adrenergic receptor blocker as a first line therapy due to
- its fast-acting relief of symptoms.
- These drugs relieve smooth muscle tone and are most effective in
- patients with early stage disease
- displaying a high smooth muscle to epithelial tissue composition.
- However, as the prostate enlarges,
- epithelial nodules predominate the tissue decreasing the likelihood
- of alpha-blocker efficacy.
+ It is clear from clinical trials of medications for BPH that personalized therapies will be needed due to
+ the highly variable responses. Typically, patients complaining of lower urinary tract symptoms are placed on
+ an alpha-adrenergic receptor blocker as a first line therapy due to its fast-acting relief of symptoms.
+ These drugs relieve smooth muscle tone and are most effective in patients with early stage disease
+ displaying a high smooth muscle to epithelial tissue composition. However, as the prostate enlarges,
+ epithelial nodules predominate the tissue decreasing the likelihood of alpha-blocker efficacy.
</p>
<p style="text-align:justify; font-size:18px">
- The second-line therapy for BPH is a 5 alpha reductase inhibitor
- (5ARI), which induces epithelial apoptosis
- by decreasing the levels of intra-prostatic dihyrotestosterone
- (DHT). This therapy is effective at reducing
+ The second-line therapy for BPH is a 5 alpha reductase inhibitor (5ARI), which induces epithelial apoptosis
+ by decreasing the levels of intra-prostatic dihyrotestosterone (DHT). This therapy is effective at reducing
prostate size by 25 percent in most patients.
</p>
<p style="text-align:justify; font-size:18px">
- Importantly, either therapy only reduces symptomatic progression by
- 34 percent, suggesting
- androgen-independent mechanisms of prostate growth and symptoms need
- to be targeted. Responses to current
- drugs are further reduced in patients with obesity, diabetes, and
- dyslipidemia.
+ Importantly, either therapy only reduces symptomatic progression by 34 percent, suggesting
+ androgen-independent mechanisms of prostate growth and symptoms need to be targeted. Responses to current
+ drugs are further reduced in patients with obesity, diabetes, and dyslipidemia.
</p>
<p style="text-align:justify; font-size:18px">
- These data suggest that there are further measures that are
- necessary for every patient, and completely
- novel measures necessary for individual patients. Our goal is to
- characterize the cellular composition of
- particular phenotypes, and more deeply understand the molecular
- changes driving these phenotypes. We use a
- combination of single cell RNA sequencing, flow cytometry, and
- immunohistochemistry on specimens from young
+ These data suggest that there are further measures that are necessary for every patient, and completely
+ novel measures necessary for individual patients. Our goal is to characterize the cellular composition of
+ particular phenotypes, and more deeply understand the molecular changes driving these phenotypes. We use a
+ combination of single cell RNA sequencing, flow cytometry, and immunohistochemistry on specimens from young
organ donors and older men with prostatic enlargement.
</p>
</div>
diff --git a/layouts/custom/sc.data.html b/layouts/custom/sc.data.html
index 56052c0..604721f 100644
--- a/layouts/custom/sc.data.html
+++ b/layouts/custom/sc.data.html
@@ -1,14 +1,14 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
<div class="content">
- {{ range .Pages.ByWeight }}
+ {{ range .Pages.ByWeight }}
<li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
- {{ end }}
+ {{ end }}
</div>
{{ partial "footer.html" . }}
\ No newline at end of file
--
GitLab