/
metadata_charts.json
1078 lines (1072 loc) · 31.1 KB
/
metadata_charts.json
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{
"sources": {
"HMP": {
"display": "HMP",
"mapping": "../../data/HMP/HMPv35_100nt.txt",
"restrict": {
"column": "#SampleID",
"values": "*",
"unique": "hostsubjectid"
}
},
"GG": {
"display": "GG",
"mapping": "../../data/GG/GG_100nt.txt",
"restrict": {
"column": "#SampleID",
"values": "*",
"unique": "HOST_SUBJECT_ID"
}
},
"PGP": {
"display": "PGP",
"mapping": "../../data/PGP/PGP_100nt.txt",
"restrict": {
"column": "#SampleID",
"values": "*",
"unique": "host_subject_id"
}
},
"AG": {
"display": "AG",
"mapping": "combined_mapping.txt",
"restrict": {
"column": "#SampleID",
"values": "*",
"unique": "HOST_SUBJECT_ID"
}
},
"AG_fecal": {
"display": "AG",
"mapping": "AG_100nt_massaged.txt",
"biom": "ag_fecal_even1k.biom",
"restrict": {
"column": "BODY_SITE",
"values": "UBERON:feces"
}
}
},
"colors": {
"c0": "#797979",
"c1": "#9e0142",
"c2": "#d53e4f",
"c3": "#f46d63",
"c4": "#fdae61",
"c5": "#fee08b",
"c6": "#ffffbf",
"c7": "#e6f598",
"c8": "#abdda4",
"c9": "#66c2a5",
"c10": "#3288bd",
"c11": "#000000"
},
"stratifications": {
"fig2_gender_strata": [
{
"name":"Unknown",
"display":"Unknown",
"color": "c0"
},
{
"name":"females",
"display":"Females",
"color": "c2"
},
{
"name":"males",
"display":"Males",
"color": "c10"
}
],
"fig2_age_strata": [
{
"name":"Unknown",
"display":"Unknown",
"color": "c0"
},
{
"name":"eighty",
"display":"80+",
"color": "c1"
},
{
"name":"seventy",
"display":"70-79",
"color": "c2"
},
{
"name":"sixty",
"display":"60-69",
"color": "c3"
},
{
"name":"fifty",
"display":"50-59",
"color": "c4"
},
{
"name":"fourty",
"display":"40-49",
"color": "c5"
},
{
"name":"thirty",
"display":"30-39",
"color": "c6"
},
{
"name":"twenty",
"display":"20-29",
"color": "c7"
},
{
"name":"teen",
"display":"13-19",
"color": "c8"
},
{
"name":"child",
"display":"3-13",
"color": "c9"
},
{
"name":"baby",
"display":"0-2",
"color": "c10"
}
],
"fig2_bmi_strata": [
{
"name":"Unk",
"display":"Unk",
"color": "c0"
},
{
"name":"vso",
"display":"VSO",
"color": "c1"
},
{
"name":"so",
"display":"SO",
"color": "c2"
},
{
"name":"mo",
"display":"MO",
"color": "c3"
},
{
"name":"o",
"display":"O",
"color": "c4"
},
{
"name":"n",
"display":"N",
"color": "c5"
},
{
"name":"u",
"display":"U",
"color": "c7"
},
{
"name":"su",
"display":"SU",
"color": "c9"
},
{
"name":"vsu",
"display":"VSU",
"color": "c10"
}
],
"fig3_diet_strata": [
{
"name":"omnivore",
"display":"Omnivore",
"color": "c11"
},
{
"name":"nrm",
"display":"No red meat",
"color": "c11"
},
{
"name":"pescetarian",
"display":"Pescetarian",
"color": "c11"
},
{
"name":"vegetarian",
"display":"Vegetarian",
"color": "c11"
},
{
"name":"vegan",
"display":"Vegan",
"color": "c11"
},
{
"name":"Unknown",
"display":"Unknown",
"color": "c11"
}
],
"fig3_exercise_strata": [
{
"name":"never",
"display":"Never",
"color": "c11"
},
{
"name":"rarely",
"display":"Rarely",
"color": "c11"
},
{
"name":"occasionally",
"display":"Occasionally",
"color": "c11"
},
{
"name":"regularly",
"display":"Regularly",
"color": "c11"
},
{
"name":"daily",
"display":"Daily",
"color": "c11"
},
{
"name":"Unknown",
"display":"Unknown",
"color": "c11"
}
],
"fig3_vitamin_strata": [
{
"name":"no",
"display":"No",
"color": "c11"
},
{
"name":"yes",
"display":"Yes",
"color": "c11"
},
{
"name":"Unknown",
"display":"Unknown",
"color": "c11"
}
],
"observation_strata": [
{
"name":"p8",
"display":"Other",
"color": "c0"
},
{
"name":"p1",
"display":"Firmicutes",
"color": "c1"
},
{
"name":"p2",
"display":"Bacteroidetes",
"color": "c2"
},
{
"name":"p3",
"display":"Proteobacteria",
"color": "c4"
},
{
"name":"p4",
"display":"Actinobacteria",
"color": "c5"
},
{
"name":"p5",
"display":"Verrucomicrobia",
"color": "c7"
},
{
"name":"p6",
"display":"Tenericutes",
"color": "c9"
},
{
"name":"p7",
"display":"Cyanobacteria",
"color": "c10"
}
]
},
"graph_sets": {
"fig3": {"subplot_shape": [4, 10]},
"fig2": {"subplot_shape": [4, 10]},
"fig6_a": {"subplot_shape": [4, 10]},
"fig6_b": {"subplot_shape": [4, 13]}
},
"graphs": [
{
"name": "fig6_a",
"title": "Antibiotic use",
"type": "stackedbar",
"scaled": false,
"legend": false,
"graph_set": "fig6_a",
"font_family": "Liberation Sans",
"ylim": [0.0, 1.0],
"ygrid": true,
"dimension": [4,5],
"x_label_rotation": 45,
"x_label_alignment": "right",
"y_label": "Fraction of the microbiome",
"format": "pdf",
"y_stratification": "observation_strata",
"@var aliases": {
"Firmicutes":"p1",
"Bacteroidetes": "p2",
"Proteobacteria":"p3",
"Actinobacteria":"p4",
"Verrucomicrobia":"p5",
"Tenericutes":"p6",
"Cyanobacteria":"p7"
},
"data": [
{
"display": "In the past week",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "ANTIBIOTIC_SELECT",
"values": [
"In the past week"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "In the past month",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "ANTIBIOTIC_SELECT",
"values": [
"In the past month"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "In the past 6 months",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "ANTIBIOTIC_SELECT",
"values": [
"In the past 6 months"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "In the past year",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "ANTIBIOTIC_SELECT",
"values": [
"In the past year"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Not in the last year",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "ANTIBIOTIC_SELECT",
"values": [
"Not in the last year"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
}]},
{
"name": "fig6_diet",
"title": "Diet type",
"type": "stackedbar",
"scaled": false,
"font_family": "Liberation Sans",
"legend": false,
"ylim": [0.0, 1.0],
"ygrid": true,
"graph_set": "fig6_a",
"dimension": [4,5],
"x_label_rotation": 45,
"x_label_alignment": "right",
"format": "pdf",
"y_stratification": "observation_strata",
"@var aliases": {
"Firmicutes":"p1",
"Bacteroidetes": "p2",
"Proteobacteria":"p3",
"Actinobacteria":"p4",
"Verrucomicrobia":"p5",
"Tenericutes":"p6",
"Cyanobacteria":"p7"
},
"data": [
{
"display": "Omnivore",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "DIET_TYPE",
"values": [
"Omnivore"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "No red meat",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "DIET_TYPE",
"values": [
"Omnivore but no red meat"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Pescetarian",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "DIET_TYPE",
"values": [
"Vegetarian but eat seafood"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Vegetarian",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "DIET_TYPE",
"values": [
"Vegetarian"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Vegan",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "DIET_TYPE",
"values": [
"Vegan"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
}]},
{
"name": "fig6_legend",
"title": "",
"type": "legend",
"legend_loc": "center left",
"legend_size": 12,
"dimension": [4,4],
"format": "pdf",
"font_family": "Liberation Sans",
"y_stratification": "observation_strata",
"@var aliases": {
"Firmicutes":"p1",
"Bacteroidetes": "p2",
"Proteobacteria":"p3",
"Actinobacteria":"p4",
"Verrucomicrobia":"p5",
"Tenericutes":"p6",
"Cyanobacteria":"p7"
}},
{
"name": "fig6_b",
"title": "Age",
"type": "stackedbar",
"y_label": "Fraction of the microbiome",
"scaled": false,
"graph_set": "fig6_b",
"font_family": "Liberation Sans",
"legend": false,
"ylim": [0.0, 1.0],
"ygrid": true,
"dimension": [4,8],
"x_label_rotation": 45,
"x_label_alignment": "right",
"format": "pdf",
"y_stratification": "observation_strata",
"@var aliases": {
"Firmicutes":"p1",
"Bacteroidetes": "p2",
"Proteobacteria":"p3",
"Actinobacteria":"p4",
"Verrucomicrobia":"p5",
"Tenericutes":"p6",
"Cyanobacteria":"p7"
},
"data": [
{
"display": "Baby",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"Baby"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Child",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"Child"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Teen",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"Teen"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "20s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"20s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "30s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"30s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "40s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"40s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "50s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"50s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "60s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"60s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "70s",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"70s"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "80+",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "AGE_CATEGORY",
"values": [
"Older than 80"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
}]},
{
"name": "fig6_exercise_frequency",
"title": "Exercise frequency",
"type": "stackedbar",
"scaled": false,
"graph_set": "fig6_b",
"legend": false,
"ylim": [0.0, 1.0],
"ygrid": true,
"font_family": "Liberation Sans",
"dimension": [4,5],
"x_label_rotation": 45,
"x_label_alignment": "right",
"format": "pdf",
"y_stratification": "observation_strata",
"@var aliases": {
"Firmicutes":"p1",
"Bacteroidetes": "p2",
"Proteobacteria":"p3",
"Actinobacteria":"p4",
"Verrucomicrobia":"p5",
"Tenericutes":"p6",
"Cyanobacteria":"p7"
},
"data": [
{
"display": "Never",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "EXERCISE_FREQUENCY",
"values": [
"Never"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Rarely",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "EXERCISE_FREQUENCY",
"values": [
"Rarely (few times/month)"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Occasionally",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "EXERCISE_FREQUENCY",
"values": [
"Occasionally (1-2 times/week)"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Regularly",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "EXERCISE_FREQUENCY",
"values": [
"Regularly (3-5 times/week)"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
},
{
"display": "Daily",
"source": "AG_fecal",
"group-by": "id",
"restrict": {
"column": "EXERCISE_FREQUENCY",
"values": [
"Daily"
]
},
"column": "@biom @taxa 1",
"aliases": "@var aliases",
"default": "p8"
}
]},
{
"name": "fig2",
"type": "stackedbar",
"title": "Gender",
"scaled": true,
"graph_set": "fig2",
"font_family": "Liberation Sans",
"fontsize": 16,
"legend": true,
"x_label_rotation": 45,
"x_label_alignment": "right",
"dimension": [4,4],
"dpi": 300,
"legend_size": 9,
"format": "pdf",
"ygrid": true,
"ylim": [0, 3500],
"y_label": "Number of Participants",
"y_stratification": "fig2_gender_strata",
"data": [
{
"display": "HMP",
"source": "HMP",
"group-by": "id",
"column": "sex",
"aliases": {
"male": "males",
"female": "females"
},
"default": "Unknown"
},
{
"display": "GG",
"source": "GG",
"group-by": "id",
"column": "SEX",
"aliases": {
"male": "males",
"female": "females"
},
"default": "Unknown"
},
{
"display": "PGP",
"source": "PGP",
"group-by": "id",
"column": "Sex/Gender",
"aliases": {
"Male": "males",
"Female": "females"
},
"default": "Unknown"
},
{
"display": "AG",
"source": "AG",
"group-by": "id",
"column": "SEX",
"aliases": {
"male": "males",
"female": "females",
"48": "females",
"47": "males"
},
"default": "Unknown"
}
]
},
{
"name": "fig2_age",
"type": "stackedbar",
"fontsize": 16,
"scaled": true,
"title": "Age",
"ygrid": true,
"legend": true,
"graph_set": "fig2",
"x_label_rotation": 45,
"x_label_alignment": "right",
"y_ticks": false,
"font_family": "Liberation Sans",
"dimension": [4,4],
"ylim": [0, 3500],
"format": "pdf",
"dpi": 300,
"legend_size": 9,
"y_stratification": "fig2_age_strata",
"@var bins": {
"80": "eighty",
"70": "seventy",
"60": "sixty",
"50": "fifty",
"40": "fourty",
"30": "thirty",
"20": "twenty",
"13": "teen",
"3": "child",
"0": "baby"
},
"data": [
{
"display": "HMP",
"source": "HMP",
"group-by": "bin",
"column": "AGE",
"bins": "@var bins",
"default": "Unknown"
},
{
"display": "GG",
"source": "GG",
"group-by": "bin",
"column": "AGE_IN_YEARS",
"bins": "@var bins",
"default": "Unknown"
},
{
"display": "PGP",
"source": "PGP",
"group-by": "id",
"column": "Age",
"aliases": {
"90-99 years":"eighty",
"80-89 years":"eighty",
"70-79 years":"seventy",
"60-69 years":"sixty",
"50-59 years":"fifty",
"40-49 years":"fourty",
"30-39 years":"thirty",
"21-29 years":"twenty"
},
"default": "Unknown"
},
{
"display": "AG",
"source": "AG",
"group-by": "bin",
"column": "AGE",
"bins": "@var bins",
"default": "Unknown"
}
]
},
{
"name": "fig2_bmi",
"type": "stackedbar",
"scaled": true,
"title": "BMI",
"fontsize": 16,
"ygrid": true,
"legend": true,
"legend_loc": "upper left",
"font_family": "Liberation Sans",
"x_label_rotation": 45,
"x_label_alignment": "right",
"y_ticks": false,
"dimension": [4,2],
"graph_set": "fig2",
"ylim": [0, 3500],
"format": "pdf",
"dpi": 300,
"legend_size": 8,
"y_stratification": "fig2_bmi_strata",
"@var bins": {
"100": "vso",
"35": "vo",
"30": "mo",
"25": "o",
"18.5": "n",
"16": "u",
"15": "su",
"1": "vsu",
"0": "Unk"
},
"data": [
{
"display": "HMP",
"source": "HMP",
"group-by": "bin",
"column": "bmi",
"bins": "@var bins",
"default": "Unk"
},
{
"display": "AG",
"source": "AG",
"group-by": "bin",
"column": "BMI",
"bins": "@var bins",
"default": "Unk"
}
]
},
{
"name": "fig3",
"type": "bar",
"x_stratification": "fig3_diet_strata",
"ylim": [0, 3000],
"graph_set": "fig3",
"dimension": [4,4],
"title": "Diet type",
"ygrid": true,
"fontsize": 16,
"font_family": "Liberation Sans",
"x_label_rotation": 45,
"x_label_alignment": "right",
"dpi": 300,