Prepare 2021 submission data with self cellxgene server

archetypes/sc.data.md

@@ -7,6 +7,7 @@ draft: true
 weight: ""
 type: "custom"
 layout: ""
+pending: false
 cellxgene: false
 cxg_link: ""
 current: true

content/sc.data/PdPgb.md

@@ -7,6 +7,7 @@ draft: false
 weight: "2"
 type: "custom"
 layout: "hu.PdPgb"
+pending: false
 cellxgene: false
 cxg_link: ""
 current: true

content/sc.data/cellxgene_huPr_Pd_all.md → content/sc.data/cellxgene_2018CellReports_huPr_Pd_all.md

 ---
 title: "Human Normal Prostate: All Cells"
 description: "As published in 2018 Cell Reports and updated in 2020 The Prostate (cellxgene)"
-name: "Human Normal Prostate: All Cells"
+name: "2018 Cell Reports: Human Normal Prostate - All Cells"
 date: 2019-12-24T21:46:39-06:00
 draft: false
-weight: "1"
+weight: "10"
 type: "custom"
 layout: "cellxgene"
+pending: false
 cellxgene: true
 cxg_link: "https://cellxgene.cziscience.com/d/dd811609-3d83-4bdb-801f-d6c6c93d1a9e.cxg/"
 current: true

content/sc.data/cellxgene_huPr_Pd_epi.md → content/sc.data/cellxgene_2018CellReports_huPr_Pd_epi.md

 ---
-title: "Human Normal Prostate: Epithelial Cells"
+title: "2018 Human Normal Prostate: Epithelial Cells"
 description: "As published in 2018 Cell Reports and updated in 2020 The Prostate (cellxgene)"
-name: "Human Normal Prostate: Epithelial Cells"
+name: "2018 Cell Reports: Human Normal Prostate - Epithelial Cells"
 date: 2019-12-24T21:46:39-06:00
 draft: false
-weight: "2"
+weight: "11"
 type: "custom"
 layout: "cellxgene"
+pending: false
 cellxgene: true
 cxg_link: "https://cellxgene.cziscience.com/d/47d05a66-7b83-4439-ad18-180d4c262f7a.cxg/"
 current: true

content/sc.data/cellxgene_huPr_Pd_fmst.md → content/sc.data/cellxgene_2018CellReports_huPr_Pd_fmst.md

 ---
-title: "Human Normal Prostate: Fibromuscular Cells"
+title: "Human Normal Prostate: Fibromuscular Stromal Cells"
 description: "As published in 2018 Cell Reports and updated in 2020 The Prostate (cellxgene)"
-name: "Human Normal Prostate: Fibromuscular Cells"
+name: "2018 Cell Reports: Human Normal Prostate - Fibromuscular Stromal Cells"
 date: 2019-12-24T21:46:39-06:00
 draft: false
-weight: "2"
+weight: "12"
 type: "custom"
+pending: false
 layout: "cellxgene"
 cellxgene: true
 cxg_link: "https://cellxgene.cziscience.com/d/e0802089-01a0-4e3a-9dbf-03eac64b15d9.cxg/"

content/sc.data/cellxgene_huPr_PdPgb_epi.md → content/sc.data/cellxgene_2020Prostate_huPr_PdPgb_epi.md

 ---
 title: "Human Normal and BPH Prostate: Epithelial Cells"
 description: "As published in 2020 Prostate (cellxgene)"
-name: "Human Normal and BPH Prostate: Epithelial Cells"
+name: "2020 Prostate: Human Normal and BPH Prostate - Epithelial Cells"
 date: 2019-12-24T21:46:39-06:00
 draft: false
-weight: "4"
+weight: "8"
 type: "custom"
+pending: false
 layout: "cellxgene"
 cellxgene: true
 cxg_link: "https://cellxgene.cziscience.com/d/599b5549-3611-41e1-884f-d5c16b2efd31.cxg/"

content/sc.data/cellxgene_muPrUr_epi.md → content/sc.data/cellxgene_2020Prostate_muPrUr_epi.md

 ---
 title: "Mouse Prostate and Urethral: Epithelial Cells"
 description: "As published in 2020 The Prostate (cellxgene)"
-name: "Mouse Prostate and Urethral: Epithelial Cells"
+name: "2020 Prostate: Mouse Prostate and Urethral - Epithelial Cells"
 date: 2019-12-24T21:46:39-06:00
 draft: false
-weight: "5"
+weight: "9"
 type: "custom"
 layout: "cellxgene"
 cellxgene: true

content/sc.data/cellxgene_2021_huPr_PdPb_all.md

+---
+title: "Human Normal and BPH Prostate: All Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Human Normal and BPH Prostates - All Cells "
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "1"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/huPr_PdPb_id_all.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_huPr_PdPb_epi.md

+---
+title: "Human Normal and BPH Prostate: Epithelial Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Human Normal and BPH Prostates - Epithelial Cells "
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "2"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/huPr_PdPb_id_epi.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_huPr_PdPb_fmst.md

+---
+title: "Human Normal and BPH Prostate: Fibromuscular Stromal Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Human Normal and BPH Prostates - Fibromuscular Stromal Cells "
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "3"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/huPr_PdPb_id_fmst.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_huPr_PdPb_leu.md

+---
+title: "Human Normal and BPH Prostate: Leukocyte Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Human Normal and BPH Prostates - Leukocyte Cells "
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "4"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/huPr_PdPb_id_leu.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_muPrUr_all.md

+---
+title: "Mouse Prostate and Urethral: All Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Mouse Prostate and Urethral - All Cells"
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "5"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/muPrUr_id_all.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_muPrUr_epi.md

+---
+title: "Mouse Prostate and Urethral: Epithelial Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Mouse Prostate and Urethral - Epithelial Cells"
+date: 2019-12-24T21:46:39-06:00
+draft: true
+weight: "5"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/muPrUr_id_epi.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/cellxgene_2021_muPrUr_fmst.md

+---
+title: "Mouse Prostate and Urethral: Fibromuscular Stromal Cells"
+description: "Manuscript Submitted (cellxgene)"
+name: "2021 Prostate Fibroblast Paper: Mouse Prostate and Urethral - Fibromuscular Stromal Cells"
+date: 2019-12-24T21:46:39-06:00
+draft: false
+weight: "5"
+type: "custom"
+layout: "cellxgene"
+pending: true
+cellxgene: true
+cxg_link: "https://cellxgene.strandlab.net/view/PublishedData/2021/muPrUr_id_fmst.h5ad/"
+current: true
+location: ""
+---
+

content/sc.data/hu.Pd.deep.md

@@ -7,6 +7,7 @@ draft: false
 weight: "1"
 type: "custom"
 layout: "hu.Pd.deep"
+pending: false
 cellxgene: false
 cxg_link: ""
 current: true

content/sc.data/muPrUr.md

@@ -7,6 +7,7 @@ draft: false
 weight: "3"
 type: "custom"
 layout: "mu.PrUr"
+pending: false
 cellxgene: false
 cxg_link: ""
 current: true

content/sc.data/repository/filters.json

+[
+    {"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 Deference"},
+    {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+]
\ No newline at end of file

layouts/custom/sc.data.html

@@ -102,12 +102,18 @@
 </div>
 <div class="content">
     <hr>
-    <h2>Visualization with <a href="https://chanzuckerberg.github.io/cellxgene/">CZI's cellxgene</a></h2>
-    {{ range where .Pages.ByWeight "Params.cellxgene" true }}
+    <h2>Visualization of Published Data with <a href="https://chanzuckerberg.github.io/cellxgene/">CZI's cellxgene</a></h2>
+    {{ range where (where .Pages.ByWeight "Params.cellxgene" true) "Params.pending" false}}
     <li><b><a href="{{ .Params.cxg_link }}" target="_blank">{{.Params.name}}</a></b></li>
     {{ end }}
     <br>
     <hr>
+    <h2><i>Visualization of Unpublished Data with <a href="https://chanzuckerberg.github.io/cellxgene/">CZI's cellxgene</a></i></h2>
+    {{ range where (where .Pages.ByWeight "Params.cellxgene" true) "Params.pending" true}}
+    <li><b><a href="{{.Permalink}}"><mark>{{.Params.name}}</mark></a></b></li>
+    {{ end }}
+    <br>
+    <hr>
     <h2>Legacy Visualization</h2>
     {{ range where .Pages.ByWeight "Params.cellxgene" false }}
     <li><b><a href="{{.Permalink}}">{{.Params.name}}</a></b></li>