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add MK/Survival Curve plot.
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set up the demo for Prism
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@nanli-emory
nanli-emory committed Nov 17, 2020
1 parent f78ba8a commit 5e61f23
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Showing 12 changed files with 551 additions and 10,988 deletions.
202 changes: 157 additions & 45 deletions config/vis-config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,55 +2,150 @@
"HEIGHT_OF_VIS_HEADER": 30,
"MARGIN_OF_VIS": [10, 10],

"UNIT_OF_GRID_VIEW": [200,200],
"UNIT_OF_GRID_VIEW": [220,200],
"MARGIN_OF_GRID_VIEW": [10, 10],
"DATA_RESOURCE_URL":"http://144.30.2.201/",

"DATA_RESOURCE_URL":"https://pathdb.cancerimagingarchive.net/pathdb/sparql?format=csv&query=prefix+%3A+%3Chttps%3A%2F%2Fbmi.stonybrookmedicine.edu%2Ftil%2Fns%2F%3E%0ASELECT+*+WHERE+{graph+%3Chttps%3A%2F%2Fbmi.stonybrookmedicine.edu%2Ftil%3E+{%0A++++%3Fsss+%3APathDBID+%3FPathDBID%3B+%3Aclinicaltrialsubjectid+%3FslideID+.+%3Fss+%3Asubmitter_id+%3Fsubmitter_id%3B+%3Apercent_pos+%3Fpercent_pos%3B+%3ATIL_classhalf+%3FTIL_classhalf%3B+%3Acollapsed_stage+%3Fcollapsed_stage%3B+%3AsurvivalB+%3FsurvivalB+.+%3Fs%0A++++++%3Asubmitter_id+%3Fsubmitter_id%3B%0A++++++%3Aajcc_pathologic_stage+%3Fajcc_pathologic_stage%3B%0A++++++%3Aprimary_diagnosis+%3Fprimary_diagnosis%3B%0A++++++%3Aprior_malignancy+%3Fprior_malignancy%3B%0A++++++%3Avital_status+%3Fvital_status%3B%0A++++++%3Avital_status+%3Fvital_status%3B%0A++++++%3ABreast_Tumor_Type+%3FBreast_Tumor_Type%3B%0A++++++%3AsurvivalA+%3FsurvivalA%3B%0A++++++%3AslideID+%3FslideID%3B%0A++++++%3APercent_TILs_in_tumor_region+%3FPercent_TILs_in_tumor_region%3B%0A++++++%3AImmune_Subtype+%3FImmune_Subtype%3B%0A++++++%3AMolwxular_Cybersort_Lymphocytes+%3FMolwxular_Cybersort_Lymphocytes%3B%0A++++++%3AGlobal_Pattern+%3FGlobal_Pattern}}",
"DATA_FORMAT":"csv",
"VISUALIZATION_VIEW_CONFIGURATION": [
{
"id": "Collection",
"title": "Collection",
"description": "Showing the number of patients in Collection",
"id": "vital_status",
"title": "Vital Status",
"description": "Showing the number of patients in Vital Status",
"chartType": "PIE_CHART",
"fields":{"x":"collection"},
"fields":{"x":"vital_status"},
"size": [1, 1],
"priority": 50
"priority": 60
},
{
"id": "tnm_stage_count",
"title": "TNM Stage Count",
"description": "Showing the number of patients in TNM Stage",
"id": "breast_tumor_type",
"title": "Breast Tumor Type",
"description": "Showing the number of patients in Vital Status",
"chartType": "PIE_CHART",
"fields":{"x":"Breast_Tumor_Type"},
"size": [1, 1],
"priority": 60
},
{
"id": "ajcc_pathologic_stage",
"title": "Pathologic Stage Count",
"description": "Showing the number of patients in Pathologic Stage",
"chartType": "BAR_CHART",
"fields":{"x":"stagelabel"},
"fields":{"x":"ajcc_pathologic_stage"},
"size": [2, 1],
"priority": 50
},
{
"id": "gender_pie",
"title": "Gender",
"id": "km_curve",
"title": "TIL Infiltration",
"description": "KM_CURVE",
"chartType": "KM_CURVE",
"fields":{
"event":{"field":"vital_status","title":"Vital Status"},
"time":{"field":"survivalB","title":"Survival","unit":"month"},
"group":{"field":"TIL_classhalf","title":"TIL Infiltration"},
"eventValue":"Dead",
"censoredValue":"Alive"

},
"size": [2, 2],
"priority": 5
},
{
"id": "basal_km_curve",
"title": "Basal KM Curve",
"description": "Basal KM Curve",
"chartType": "KM_CURVE",
"fields":{
"event":{"field":"vital_status","title":"Vital Status"},
"time":{"field":"survivalB","title":"Survival","unit":"month"},
"group":{"field":"TIL_classhalf","title":"TIL Infiltration"},
"eventValue":"Dead",
"censoredValue":"Alive"
},
"filter":{"field":"Breast_Tumor_Type","value":"Basal"},
"size": [2, 2],
"priority": 5
},{
"id": "her2_km_curve",
"title": "Her2 KM Curve",
"description": "Her2 KM Curve",
"chartType": "KM_CURVE",
"fields":{
"event":{"field":"vital_status","title":"Vital Status"},
"time":{"field":"survivalB","title":"Survival","unit":"month"},
"group":{"field":"TIL_classhalf","title":"TIL Infiltration"},
"eventValue":"Dead",
"censoredValue":"Alive"
},
"filter":{"field":"Breast_Tumor_Type","value":"Her2"},
"size": [2, 2],
"priority": 5
},{
"id": "luma_km_curve",
"title": "LumaA KM Curve",
"description": "LumaA KM Curve",
"chartType": "KM_CURVE",
"fields":{
"event":{"field":"vital_status","title":"Vital Status"},
"time":{"field":"survivalB","title":"Survival","unit":"month"},
"group":{"field":"TIL_classhalf","title":"TIL Infiltration"},
"eventValue":"Dead",
"censoredValue":"Alive"
},
"filter":{"field":"Breast_Tumor_Type","value":"LumA"},
"size": [2, 2],
"priority": 5
},{
"id": "lumb_km_curve",
"title": "LumB KM Curve",
"description": "LumB KM Curve",
"chartType": "KM_CURVE",
"fields":{
"event":{"field":"vital_status","title":"Vital Status"},
"time":{"field":"survivalB","title":"Survival","unit":"month"},
"group":{"field":"TIL_classhalf","title":"TIL Infiltration"},
"eventValue":"Dead",
"censoredValue":"Alive"
},
"filter":{"field":"Breast_Tumor_Type","value":"LumB"},
"size": [2, 2],
"priority": 5
},
{
"id": "immune_subtype",
"title": "Immune Subtype",
"description": "Showing the number of patients in gender",
"chartType": "PIE_CHART",
"fields":{"x":"sexlabel"},
"chartType": "BAR_CHART",
"fields":{"x":"Immune_Subtype"},
"size": [1, 1],
"priority": 50
},
{
"id": "disease_type_count",
"title": "Disease Type Count",
"description": "Showing the number of patients in disease type",
"id": "global_pattern",
"title": "Global Pattern",
"description": "Showing the number of patients in gender",
"chartType": "HORIZONTAL_BAR_CHART",
"fields":{"y":"Global_Pattern"},
"size": [1, 1],
"priority": 10
},
{
"id": "primary_diagnosis",
"title": "Primary Diagnosis",
"description": "Showing the number of patients in primary diagnosis",
"chartType": "HORIZONTAL_BAR_CHART",
"fields":{"y":"disease_type"},
"fields":{"y":"primary_diagnosis"},
"size": [2, 2],
"priority": 10
},
"priority": 20
},
{
"id": "age_age_scatter",
"title": "Age vs Age Time",
"id": "TILPercent_survivalA_lymph_scatter",
"title": "TILs vs survivalA vs Lymph",
"description": "Showing the age and Age in scatter plot",
"chartType": "SCATTER_CHART",
"fields":{"x":"age","y":"age","z":"age"},
"fields":{"x":"Percent_TILs_in_tumor_region","y":"survivalA","z":"Molwxular_Cybersort_Lymphocytes"},
"size": [2, 2],
"priority": 10
"priority": 30
},
{
"id":"clinical_data_table",
Expand All @@ -59,37 +154,54 @@
"chartType": "VIS_DATA_TABLE",
"fields":[
{
"dataKey":"collection",
"label":"Collection",
"width":0.13
"dataKey":"submitter_id",
"label":"ID",
"width":0.1
},
{
"dataKey":"patient_id",
"label":"Patient ID",
"width":0.08
"dataKey":"slideID",
"label":"Slide ID",
"link":{
"url":"https://pathdb.cancerimagingarchive.net/caMicroscope/apps/viewer/viewer.html?mode=pathdb&slideId=",
"field":"PathDBID"
},
"width":0.1
},
{
"dataKey":"disease_type",
"label":"Disease",
"width":0.22
"dataKey":"ajcc_pathologic_stage",
"label":"Pathologic Stage",
"width":0.1
},
{
"dataKey":"location",
"label":"Location",
"width":0.18
"dataKey":"vital_status",
"label":"Vital Status",
"width":0.08
},
{
"dataKey":"age",
"label":"Age",
"width":0.05
"dataKey":"Breast_Tumor_Type",
"label":"Breast Tumor Type",
"width":0.08
},
{
"dataKey":"survivalA",
"label":"Survival A",
"width":0.08
},{
"dataKey":"stagelabel",
"label":"Stage",
"dataKey":"Percent_TILs_in_tumor_region",
"label":"TILs Percent",
"width":0.08
},{
"dataKey":"sexlabel",
"label":"Gender",
"dataKey":"Immune_Subtype",
"label":"Immune Subtype",
"width":0.05
},{
"dataKey":"Molwxular_Cybersort_Lymphocytes",
"label":"Lymphocytes",
"width":0.08
},{
"dataKey":"Global_Pattern",
"label":"Global Pattern",
"width":0.15
}],
"size": [4, 2],
"priority": 70
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