Published
Edited
Apr 6, 2022
1 fork
byIndividual = d3.tsv(
"https://gist.githubusercontent.com/Mbrownshoes/e5b5bf4f9767d6762db3848d9fac749e/raw/73e0583e2cec2c888c9d07466e58f6e95c234930/OTU_table.tsv"
)
byIndividual.columns
byIndividual[0]
// convert wide to long
longData = {
// helpful http://jonathansoma.com/tutorials/d3/wide-vs-long-data/
let long_data = [];
byIndividual.forEach(row => {
// Loop through all of the columns, and for each column
// make a new row
Object.keys(row).forEach(function(colname) {
// Ignore 'State' and 'Value' columns
if (colname == "#OTU ID" || colname == "taxonomy") {
return;
}
let heir = row["taxonomy"].split(";");
long_data.push({
Indv: row["#OTU ID"],
Value: row[colname],
Sample: colname,
kingdom: heir[0].replace(' ', ''),
phylum: heir[1].replace(' ', ''),
class: heir[2].replace(' ', ''),
order: heir[3].replace(' ', ''),
family: heir[4].replace(' ', ''),
genus: heir[5].replace(' ', ''),
species: heir[6].replace(' ', ''),
taxonomy: row["taxonomy"]
});
});
// return row;
});
return long_data;
}
longData
fakeSites
joinedDataFake = {
let c = _.cloneDeep(longData);
c.forEach(function(individual) {
var result = fakeSites.filter(function(sample) {
return sample.SampleID === individual.Sample;
});
// delete article.brand_id;
// console.log(result[0]);
individual.month =
result[0] !== undefined ? result[0].Collection_month : null;
individual.site = result[0] !== undefined ? result[0].ARMS_number : null;
});
// console.log(c.filter(d => d.phylum === " p__Mollusca"));
return c.filter(
d =>
d.site === map &&
d.phylum === "p__Mollusca" &&
d.order !== "o__Neoloricata" &&
d.order !== "o__undef_Gastropoda"
);
// c.age = +c.age;
// c.salary = +c.salary;
return c.sort(function(a,b) { return a.month.toLowerCase().localeCompare(b.month.toLowerCase()) });
}
individual
chartData = {
const sums = d3
.nest()
// .key(d => d.site)
.key(d => d.month)
.key(d => d.species.replace("s___", "").replace("s__", ""))
.rollup(v => d3.sum(v, d => d.Value))
.object(joinedDataFake);
// return sums;
let newDat = [];
Object.keys(sums).forEach(d => {
// console.log(sums[d]);
sums[d].month = d;
newDat.push(sums[d]);
});
newDat["columns"] = speciesListFake;
let t;
let i;
newDat.forEach(d => {
for (i = 1, t = 0; i < speciesListFake.length; ++i)
t += d[speciesListFake[i]] = +d[speciesListFake[i]];
d.total = t;
});
return newDat.sort(function(a, b) {
return a.month.toLowerCase().localeCompare(b.month.toLowerCase());
});
}
d3
.nest()
// .key(d => d.site)
.key(d => d.month)
.key(d => d.species.replace("s___", "").replace("s__", ""))
.rollup(v => d3.sum(v, d => d.Value))
.object(joinedDataFake)
joinedDataFake[0]
groupSum(longData, d => d.taxonomy, d => Number(d.Value))
nest(longData, d => d.Sample, d => d.taxonomy)
groupSum(byIndividual, d => d.taxonomy, d => d["ARMS9-M-106"])
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