From 5e61f23e8362036a6c415f107b8666179f7378e1 Mon Sep 17 00:00:00 2001 From: Nan Li Date: Mon, 16 Nov 2020 22:17:21 -0500 Subject: [PATCH] add `MK/Survival Curve` plot. set up the demo for Prism --- config/vis-config.json | 202 +- data/demo.json | 10780 ---------------- .../VisGridItemContent/VisGridItemContent.js | 11 +- .../component/VisualTools/Chart/BarChart.js | 31 - source/component/VisualTools/Chart/KMCurve.js | 240 + .../component/VisualTools/Chart/PieChart.js | 1 - .../VisualTools/Chart/ScatterChart.js | 4 +- source/component/VisualTools/Chart/style.css | 5 + .../VisualTools/VisDataTable/VisDataTable.js | 10 + .../VisualTools/VisTypeComponents.js | 3 +- source/component/VisualTools/VisTypeEnum.json | 1 + source/index.js | 251 +- 12 files changed, 551 insertions(+), 10988 deletions(-) delete mode 100644 data/demo.json create mode 100644 source/component/VisualTools/Chart/KMCurve.js diff --git a/config/vis-config.json b/config/vis-config.json index 1afcac9..6848333 100644 --- a/config/vis-config.json +++ b/config/vis-config.json @@ -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", @@ -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 diff --git a/data/demo.json b/data/demo.json deleted file mode 100644 index 5d0a772..0000000 --- a/data/demo.json +++ /dev/null @@ -1,10780 +0,0 @@ -[ - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-001", - "Age": 78, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Large Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 16.91122639 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-002", - "Age": 83, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 36.63093253 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-003", - "Age": 68, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Large Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 15.891143 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-004", - "Age": 70, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage II", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 48.52820321 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-005", - "Age": 80, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 37.83168034 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-006", - "Age": 73, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 31.3484151 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-007", - "Age": 81, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 40.84594974 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-008", - "Age": 71, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Adenocarcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 41.42108539 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-009", - "Age": 56, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 13.7165436 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-010", - "Age": 71, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": -1 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-011", - "Age": 64, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 49.77924603 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-012", - "Age": 71, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 8.245498795 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-013", - "Age": 65, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Non-Small Cell Lung Cancer (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": -1 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-014", - "Age": 66, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 26.19203473 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-015", - "Age": 71, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Large Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 31.69619794 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-016", - "Age": 79, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Non-Small Cell Lung Cancer (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 35.41364858 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-017", - "Age": 73, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Large Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 0.5701499852 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-018", - "Age": 82, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage II", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 33.07221982 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-019", - "Age": 74, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Non-Small Cell Lung Cancer (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 14.41875725 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-020", - "Age": 76, - "Vital_Status": "dead", - "GDC_primary_diagnosis": -1, - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 21.95604426 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-021", - "Age": 54, - "Vital_Status": "dead", - "GDC_primary_diagnosis": -1, - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 43.31617147 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-022", - "Age": 78, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 7.33262746 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-023", - "Age": 53, - "Vital_Status": "dead", - "GDC_primary_diagnosis": -1, - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 17.48500335 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-024", - "Age": 75, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Adenocarcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 6.781909565 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-025", - "Age": 68, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Adenocarcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 1.87374939 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - "Patient_ID": "LUNG1-026", - "Age": 70, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Adenocarcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": -1, - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "Yes", - "Has_NM": "No", - "Has_PT": "No", - "Has_Pathology": "No", - "Modality": "CT, RTSTRUCT", - "Survival_Time": 48.54387608 - }, - { - "Collection": "NSCLC-Radiomics-Lung1", - 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}, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-51-4079", - "Age": 73, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 12.80185779 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-51-4080", - "Age": 65, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Basaloid Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IIIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 5.45711602 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-51-6867", - "Age": 72, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage I", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 10.01539218 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2695", - "Age": 74, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Basaloid Squamous Cell Carcinoma", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2696", - "Age": 76, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 4.227554149 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2710", - "Age": 67, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2711", - "Age": 64, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Lower", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2712", - "Age": 79, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 17.19345461 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2715", - "Age": 52, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 0.6869592052 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2716", - "Age": 39, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Papillary Squamous Cell Carcinoma", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2719", - "Age": 83, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2721", - "Age": 73, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2722", - "Age": 66, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2723", - "Age": 74, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Middle", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2724", - "Age": 47, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "Bronchial", - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2725", - "Age": 74, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-60-2726", - "Age": 56, - "Vital_Status": "dead", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Middle", - "TNM-Stage": "Stage IIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": 36.60716018 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-92-7340", - "Age": 45, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-92-7341", - "Age": 71, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-92-8063", - "Age": 52, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Upper", - "TNM-Stage": "Stage IIIA", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-92-8064", - "Age": 58, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Male", - "Neoplasm_A-1tomic_Subdivision_-1me_": "R-Upper", - "TNM-Stage": "Stage IB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - }, - { - "Collection": "TCGA-LUSC", - "Patient_ID": "TCGA-92-8065", - "Age": 74, - "Vital_Status": "alive", - "GDC_primary_diagnosis": "Lung Squamous Cell Carcinoma (NOS)", - "Gdc_gender": "Female", - "Neoplasm_A-1tomic_Subdivision_-1me_": "L-Lower", - "TNM-Stage": "Stage IIB", - "Has_CT": "Yes", - "Has_RTSTRUCT": "No", - "Has_NM": "Yes", - "Has_PT": "Yes", - "Has_Pathology": "Yes", - "Modality": "CT, NM, PT, Pathology", - "Survival_Time": -1 - } -] diff --git a/source/component/Layout/VisGridView/VisGridItem/VisGridItemContent/VisGridItemContent.js b/source/component/Layout/VisGridView/VisGridItem/VisGridItemContent/VisGridItemContent.js index f143f0e..a8a5806 100644 --- a/source/component/Layout/VisGridView/VisGridItem/VisGridItemContent/VisGridItemContent.js +++ b/source/component/Layout/VisGridView/VisGridItem/VisGridItemContent/VisGridItemContent.js @@ -15,6 +15,9 @@ const PieChart = React.lazy(() => const BarChart = React.lazy(() => import("../../../../VisualTools/Chart/BarChart") ); +const KMCurve = React.lazy(() => + import("../../../../VisualTools/Chart/KMCurve") +); const HorizontalBarChart = React.lazy(() => import("../../../../VisualTools/Chart/HorizontalBarChart") ); @@ -68,9 +71,13 @@ export default class VisGridItemContent extends Component { component = ; break; - case "HorizontalBarChart": - component = ; + break; + case "HorizontalBarChart": + component = ; break; case "VisDataTable": component = ); - return ( -
- - {this.state.bars.map((d, i) => ( - - ))} - - - - - - -
- ); } } diff --git a/source/component/VisualTools/Chart/KMCurve.js b/source/component/VisualTools/Chart/KMCurve.js new file mode 100644 index 0000000..d304887 --- /dev/null +++ b/source/component/VisualTools/Chart/KMCurve.js @@ -0,0 +1,240 @@ +import React, { Component } from 'react' +import {isEquivalent} from '../../../common/utils.js' +import * as d3 from "d3"; + +function getRandomIntInclusive(min, max) { + min = Math.ceil(min); + max = Math.floor(max); + return Math.floor(Math.random() * (max - min + 1) + min); //The maximum is inclusive and the minimum is inclusive +} +function isUndefined(d){ + return d==undefined||d==null||(typeof d === 'string' && d.toLowerCase()==`na`) +} +export default class KMCurve extends Component { + constructor(props) { + super(props); + this.self = React.createRef(); + this.maxTime = Number.NEGATIVE_INFINITY; + this.state = { + margin: {top: 35, right: 20, bottom: 45, left: 45}, + loading:true, + error:null + } + if(this.props.filter) { + this.state.data = this.transform(this.props.data.filter(d=>d[this.props.filter.field]==this.props.filter.value), this.props.fields); + }else{ + this.state.data = this.transform(this.props.data, this.props.fields); + } + + + console.log(this.state.data) + console.log(this.maxTime) + // this.state.data = { + // l1:generateData(), + // l2:generateData() + // } + // console.log("KM Data",this.state.data); + // //this.state.horizontal = true; + } + transform(data,field){ + const event_value = field.eventValue; + const censored_value = field.censoredValue; + const group = field.group.field; + const time = field.time.field; + const event = field.event.field; + + + data = data.filter(d=>d.collapsed_stage!='stage_x/NR'&&!isUndefined(d[time])&&!isUndefined(d[event])&&!isUndefined(d[group])) + this.maxTime = Math.max(...data.map(d=>d[time])); + const groups = d3.nest().key(d=>d[group]).entries(data) + const rs = [] + groups.forEach(g=>{ + const key = g.key; + let risk = g.values.length; + const values = d3.nest() + .key(d=> +d[time]) + .sortKeys((a,b)=>(+a)-(+b)) + .rollup(function(v) { + return { + event:v.filter(d=>d[event]==event_value).length, + censor:v.filter(d=>d[event]==censored_value).length + }; + }) + .entries(g.values); + let p = 1; + const points = []; + values.forEach(d=>{ + const time = +d.key; + const e = d.value.event; + const c = d.value.censor; + if(time<0) return; + if(e > 0){ + p *= (1 - e/risk) + const censored = false; + points.push({p, time, censored}) + } + if(c > 0){ + const censored = true; + points.push({p, time, censored}) + } + risk -= (e + c); + }) + rs.push({key,points}) + + }) + + return rs; + + } + shouldComponentUpdate ( nextProps, nextState ) { + // TODO LIST + console.log('KMCurve shouldComponentUpdate') + //console.log(nextProps.filters, this.props.filters) + // const flag = isEquivalent(nextProps.filters, this.props.filters); + // console.log(flag) + return true; + } + drawLine(viewer, points, color){ + const line = d3.line() + .curve(d3.curveStepAfter) + .x(d=> this.xScale(d.time)) + .y(d=> this.yScale(d.p)); + viewer.append("path") + .datum(points) + .attr("class", "line") + .style("stroke", color) + .attr("d", line); + + + points.forEach(point=>{ + if(point.censored){ + const p = [{ + p:point.p-0.015, + time:point.time, + },{ + p:point.p+0.015, + time:point.time, + }] + viewer.append("path") + .datum(p) + .attr("class", "mark") + .style("stroke", color) + .attr("d", line); + } + }) + + + } + + drawCensoredMark(viewer , point, color){ + + } + + drawKMCurve(viewer, d) { + + // draw lines + this.drawLine(viewer, d.points, this.color(d.key)) + // draw marks + } + + componentDidUpdate() { + console.log('componentDidUpdate') + } + componentDidMount() { + console.log('KM Curve') + const rect = this.self.current.getBoundingClientRect(); + const innerWidth = rect.width - this.state.margin.left - this.state.margin.right; + const innerHeight = rect.height - this.state.margin.top - this.state.margin.bottom; + // create svg + const svg = d3.select(this.self.current) + .append("svg") + .attr("width", rect.width) + .attr("height", rect.height) + // create viewer + const viewer = svg.append("g") + .attr("transform", "translate(" + this.state.margin.left + "," + this.state.margin.top + ")"); + // + this.xScale = d3.scaleLinear() + .domain([0, this.maxTime]) + .range([0, innerWidth]) + + this.yScale = d3.scaleLinear() + .domain([0, 1]) + .range([innerHeight, 0]) + + this.color = d3.scaleOrdinal() + .domain(this.state.data.map(d => d.key)) + .range(d3.quantize(t => d3.interpolateSpectral(t), this.state.data.length)) + + + + + const xaxisGroup = viewer.append("g") + .attr("transform", "translate(0," + innerHeight + ")") + .call(d3.axisBottom(this.xScale).ticks(4)); //.tickSize(-innerWidth)); + xaxisGroup.append('text') + .attr('y', 30) + .attr('x', innerWidth/2) + .attr('fill','black') + .attr('font-size',13) + .text(`Time ${this.props.fields.time.unit?`(${this.props.fields.time.unit})`:''}`) + + // add the y Axis + const yaxisGroup = viewer.append("g") + .call(d3.axisLeft(this.yScale).ticks(4)); // .tickSize(-innerWidth) + yaxisGroup.append('text') + .attr('y', -30) + .attr('x', -innerHeight/3) + .attr('fill','black') + .attr('font-size',13) + .attr("transform", "rotate(-90)") + .text(`Survival Probability`) + + this.state.data.forEach(d=>this.drawKMCurve(viewer,d)) + + + const height = 0; + const width = 15; + var nodeWidth = (d) => d.getBBox().width; + const legend = svg.append('g') + .attr('class', 'legend') + .attr('transform', `translate(${this.state.margin.left+innerWidth/2},0)`); + + const lg = legend.selectAll('g') + .data(this.state.data) + .enter() + .append('g') + .attr('transform', (d,i) => `translate(${i * 100},${height + 15})`); + + lg.append('rect') + .style('fill', d => this.color(d.key)) + .attr('x', 0) + .attr('y', 0) + .attr('width', 10) + .attr('height', 10); + + lg.append('text') + .style('font-family', 'Georgia') + .style('font-size', '13px') + .attr('x', 17.5) + .attr('y', 10) + .text(d => d.key); + + let offset = 0; + lg.attr('transform', function(d, i) { + let x = offset; + offset += nodeWidth(this) + 10; + return `translate(${x},${height + 10})`; + }); + } + + render() { + return ( +
+ ); + } +} diff --git a/source/component/VisualTools/Chart/PieChart.js b/source/component/VisualTools/Chart/PieChart.js index 3d055b9..701631c 100644 --- a/source/component/VisualTools/Chart/PieChart.js +++ b/source/component/VisualTools/Chart/PieChart.js @@ -45,7 +45,6 @@ export default class PieChart extends Component { componentDidMount() { const rect = this.self.current.getBoundingClientRect(); - const innerWidth = rect.width - this.state.margin.left - this.state.margin.right; const innerHeight = rect.height - this.state.margin.top - this.state.margin.bottom; const radius = Math.min(innerWidth, innerHeight)/2 diff --git a/source/component/VisualTools/Chart/ScatterChart.js b/source/component/VisualTools/Chart/ScatterChart.js index e4e2aca..33743ee 100644 --- a/source/component/VisualTools/Chart/ScatterChart.js +++ b/source/component/VisualTools/Chart/ScatterChart.js @@ -67,11 +67,11 @@ export default class ScatterChart extends Component { viewer.append("g") .attr("transform", "translate(0," + innerHeight + ")") - .call(d3.axisBottom(this.xScale).tickSize(-innerWidth)); + .call(d3.axisBottom(this.xScale).tickSize(-innerHeight)); // add the y Axis viewer.append("g") - .call(d3.axisLeft(this.yScale).tickSize(-innerHeight)); + .call(d3.axisLeft(this.yScale).tickSize(-innerWidth)); diff --git a/source/component/VisualTools/Chart/style.css b/source/component/VisualTools/Chart/style.css index 946e1d8..f114086 100644 --- a/source/component/VisualTools/Chart/style.css +++ b/source/component/VisualTools/Chart/style.css @@ -36,3 +36,8 @@ text.label { stroke-dasharray: 1; stroke-opacity: 1; } +.line { + fill: none; + stroke: steelblue; + stroke-width: 2px; +} \ No newline at end of file diff --git a/source/component/VisualTools/VisDataTable/VisDataTable.js b/source/component/VisualTools/VisDataTable/VisDataTable.js index cdd45e7..fa876bc 100644 --- a/source/component/VisualTools/VisDataTable/VisDataTable.js +++ b/source/component/VisualTools/VisDataTable/VisDataTable.js @@ -29,6 +29,16 @@ export default class VisDataTable extends Component { key={id} dataKey={f.dataKey} label={f.label} width={width*f.width} + cellRenderer = {(d)=>{ + + if(f.link) { + const URL = `${f.link.url+d.rowData[f.link.field]}` + return {d.cellData}; + } else { + return d.cellData; + } + + }} />)} )} diff --git a/source/component/VisualTools/VisTypeComponents.js b/source/component/VisualTools/VisTypeComponents.js index ab8204f..21e8cab 100644 --- a/source/component/VisualTools/VisTypeComponents.js +++ b/source/component/VisualTools/VisTypeComponents.js @@ -11,7 +11,8 @@ VisTypeComponents.PIE_CHART = "PieChart"; VisTypeComponents.BAR_CHART = "BarChart"; VisTypeComponents.HORIZONTAL_BAR_CHART ="HorizontalBarChart"; VisTypeComponents.SCATTER_CHART = "ScatterChart"; +VisTypeComponents.KM_CURVE = "KMCurve"; VisTypeComponents.VIS_DATA_TABLE = "VisDataTable"; -VisTypeComponents.VEGA_LITE_PLOT = "VegaLitePlot" +VisTypeComponents.VEGA_LITE_PLOT = "VegaLitePlot"; export default VisTypeComponents \ No newline at end of file diff --git a/source/component/VisualTools/VisTypeEnum.json b/source/component/VisualTools/VisTypeEnum.json index 958e69d..9fb86b4 100644 --- a/source/component/VisualTools/VisTypeEnum.json +++ b/source/component/VisualTools/VisTypeEnum.json @@ -2,6 +2,7 @@ "PIE_CHART": "PIE_CHART", "BAR_CHART": "BAR_CHART", "HORIZONTAL_BAR_CHART" : "HORIZONTAL_BAR_CHART", + "KM_CURVE": "KM_CURVE", "SCATTER_CHART": "SCATTER_CHART", "VIS_DATA_TABLE": "VIS_DATA_TABLE", "VEGA_LITE_PLOT":"VEGA_LITE_PLOT" diff --git a/source/index.js b/source/index.js index f7779c4..e75a936 100644 --- a/source/index.js +++ b/source/index.js @@ -9,6 +9,7 @@ import Spinner from 'react-bootstrap/Spinner' import VisGridView from "./component/Layout/VisGridView/VisGridView.js"; import ProgressBar from 'react-bootstrap/ProgressBar' import FilterOperationPanel from './component/FilterOperationPanel/FilterOperationPanel.js' +import * as d3 from "d3"; import { Responsive, WidthProvider, @@ -29,73 +30,60 @@ import "./style/main.scss"; import 'react-virtualized/styles.css'; // config for view grid and vis compoments import _CONFIG_ from "../config/vis-config.json"; + // var __DM = null; -// var __DS = null; +function isNumeric(str) { + if (typeof str != "string") return false // we only process strings! + return !isNaN(str) && // use type coercion to parse the _entirety_ of the string (`parseFloat` alone does not do this)... + !isNaN(parseFloat(str)) // ...and ensure strings of whitespace fail +} +function covertRaw(elt){ + for(let key in elt){ + const raw = elt[key]; + if(isNumeric(raw)){ + elt[key] = +raw; + } else if(raw == 'true'||raw == 'false' ){ + elt[key] = raw=='true' ? true : false; + } + } + return elt; +} -function filterData(data, filters){ +function filterData(data, filters) { return data.filter(record => { - for (let filter of filters){ + for (let filter of filters) { const operation = filter.operation; const val = record[filter.field]; - - // switch (oprs) { // eq, gt, gte, in, lt, lte, ne, nin - // case 'eq': - // if(val == filter.values) - // break; - // case 'gt': - // if(val > filter.values) - // break; - // case 'gte': - // if(val >= filter.values) return true; - // break; - // case 'lt': - // if(val < filter.values) return true; - // break; - // case 'lte': - // if(val <= filter.values) return true; - // break; - // case 'ne': - // if(val != filter.values) return true; - // break; - // case 'in': - // if(filter.values.some(v=> val == v)) return true; - // break; - // case 'nin': - // if(!filter.values.some(v=> val == v)) return true; - // break; - // case 'range': - // if() return true; - // break; - // } + let broken = false - if (!broken && operation==='eq'){ + if (!broken && operation === 'eq') { broken = broken || val !== filter.values } - if (!broken && operation==='gt'){ + if (!broken && operation === 'gt') { broken = broken || val <= filter.values } - if (!broken && operation==='gte'){ + if (!broken && operation === 'gte') { broken = broken || val < filter.values } - if (!broken && operation==='lt'){ + if (!broken && operation === 'lt') { broken = broken || val >= filter.values } - if (!broken && operation==='lte'){ + if (!broken && operation === 'lte') { broken = broken || val > filter.values - } - if (!broken && operation==='ne'){ + } + if (!broken && operation === 'ne') { broken = broken || val === filter.values - } - if (!broken && operation==='in'){ - broken = broken || !filter.values.some(v=> val == v) - } - if (!broken && operation==='nin'){ - broken = broken || filter.values.some(v=> val == v) - } - if (!broken && operation==='range'){ - broken = broken || filter.values[0]>val || filter.values[1] val == v) + } + if (!broken && operation === 'nin') { + broken = broken || filter.values.some(v => val == v) + } + if (!broken && operation === 'range') { + broken = broken || filter.values[0] > val || filter.values[1] < val + } + if (broken) { return false } } @@ -114,7 +102,7 @@ class App extends React.Component { filterOperators: "AND", // "OR" filters: [] }; - + } // { // id: @@ -123,122 +111,133 @@ class App extends React.Component { // value: value, value, value, list, value, value, value, list, [] // } addFiltersHandler(filters) { - + const old_filters = [...this.state.filters]; - + // remove first - let new_filters = old_filters.filter(of=> filters.some(nf => !(of.id == nf.id))) + let new_filters = old_filters.filter(of => filters.some(nf => !(of.id == nf.id))) + - // add - new_filters = [...new_filters,...filters] + new_filters = [...new_filters, ...filters] //filters.push(filter) - + // do filter - const dataset_afterFilter = filterData(this.state.data,new_filters); - - this.setState({filterData:dataset_afterFilter, filters: new_filters}) + const dataset_afterFilter = filterData(this.state.data, new_filters); + + this.setState({ filterData: dataset_afterFilter, filters: new_filters }) } - - removeFiltersHandler(id,isIndex=false){ + + removeFiltersHandler(id, isIndex = false) { // remove all filter - if(id==='ALL'){ - this.setState({filterData:[], filters: []}); + if (id === 'ALL') { + this.setState({ filterData: [], filters: [] }); return; } const old_filters = [...this.state.filters]; - console.log('old',old_filters) + console.log('old', old_filters) let new_filters = []; - if(isIndex){ - new_filters = old_filters.filter((f,idx)=>idx!=id) - }else{ - new_filters = old_filters.filter(of=> of.id !== id) + if (isIndex) { + new_filters = old_filters.filter((f, idx) => idx != id) + } else { + new_filters = old_filters.filter(of => of.id !== id) } - - console.log('new',new_filters) - if(new_filters.length <= 0){ - this.setState({filterData:[], filters: []}); + + console.log('new', new_filters) + if (new_filters.length <= 0) { + this.setState({ filterData: [], filters: [] }); return; } const dataset_afterFilter = filterData(this.state.data, new_filters); - this.setState({filterData:dataset_afterFilter, filters: new_filters}) + this.setState({ filterData: dataset_afterFilter, filters: new_filters }) } componentDidMount() { - fetch(_CONFIG_.DATA_RESOURCE_URL,{ - mode: 'cors' - }) - .then(res=>res.json()) - .then(data=> - { - // data.forEach(d => {// clear up null value - // if(d.disease_type == null) d.disease_type = 'NA' - // if(d.sexlabel == null) d.sexlabel = 'NA' - // if(d.age == null) d.age = 'NA' - // if(d.stagelabel == null) d.stagelabel = 'NA' - // }) - return data;}) - .then((data) => { + if (_CONFIG_.DATA_FORMAT === 'csv') { + d3.csv(_CONFIG_.DATA_RESOURCE_URL,d=>covertRaw(d)).then(data=>{ + console.log('data',data) + this.setState({ + isLoaded: true, + data: data + }); + }) + + } else if (_CONFIG_.DATA_FORMAT === 'json') { + fetch(_CONFIG_.DATA_RESOURCE_URL, { + mode: 'cors' + }).then(res => res.json()).then(data => { + // TODO need a replace method to replace null, undefined etc. + data.forEach(d => {// clear up null value + if (d.disease_type == null) d.disease_type = 'NA' + if (d.sexlabel == null) d.sexlabel = 'NA' + if (d.age == null) d.age = 'NA' + if (d.stagelabel == null) d.stagelabel = 'NA' + }) + return data; + }) + .then((data) => { console.log(data) this.setState({ isLoaded: true, data: data }); }, - // Note: it's important to handle errors here - // instead of a catch() block so that we don't swallow - // exceptions from actual bugs in components. - (error) => { - console.log('error',error) - this.setState({ - isLoaded: true, - error - }); - } - ) + // Note: it's important to handle errors here + // instead of a catch() block so that we don't swallow + // exceptions from actual bugs in components. + (error) => { + console.log('error', error) + this.setState({ + isLoaded: true, + error + }); + } + ) + } + } render() { const { error, isLoaded, data, filterData, filters } = this.state; const progressAttrs = { - now:data.length, - label:`${data.length}/${data.length}` + now: data.length, + label: `${data.length}/${data.length}` }; - if(filters.length > 0){ + if (filters.length > 0) { progressAttrs.now = filterData.length; progressAttrs.label = `${filterData.length}/${data.length}` } if (error) { return
Error: {error.message}
; } else if (!isLoaded) { - return
+ return
- + - Loading... + Loading...
; } else { return (
-
+ {/*
+ + + + ); } }