spfilter = d3bf.loadfilters("emap_filters.txt",
form.getvalue("spfilter", "none"))
level = form.getvalue("level")
fmethod = form.getvalue("fmethod", "PCA")
color = form.getvalue("color", "none")
shape = form.getvalue("shape", "none")
labels = form.getvalue("labels", "none")
resolution = form.getvalue("resolution", "low")
ilevel = int(level)
(data, volumes, mn, ml) = d3bf.loaddata("emap.txt")
(tags, tkeys) = d3bf.loadtags("emap_tags.txt", volumes)
(kdict, kdnames, kgnames, knorder,
kdata) = d3bf.loadtaxonomy(data, ml, spfilter, ilevel)
(findex, mtags) = d3bf.processtags_m(volumes, tags, dfilter)
(edata, site_ids, species_ids) = d3bf.load_edata_m(data, ilevel, mn, ml, kdict,
volumes, findex, kdnames)
aedata = np.array(edata, dtype=float)
aenorm = np.sum(aedata, axis=1)
aedata /= aenorm.reshape(len(edata), 1)
rev = 0
if fmethod == "PCA (sklearn)": #or fmethod == "MDS (sklearn)":
rev = 1
cdata = d3bf.calc_distances(edata, aedata, dmethod, kdata, knorder, rev)
adist = np.array(cdata)
amax = np.amax(adist)
adist /= amax
alabels = ["", ""]
(tags, tkeys) = d3bf.loadtags("emap_tags.txt", volumes)
ilevel = int(level)
(kdict, kdnames, kgnames, knorder,
kdata) = d3bf.loadtaxonomy(data, ml, spfilter, ilevel)
valhighlight = 0. if numhighlight == "all" else 0.01 * float(numhighlight[:-1])
if dgroup != "none":
(findex, gtags) = d3bf.processtags(volumes, tags, dfilter, dgroup)
edata = d3bf.load_edata(data, ilevel, ml, kdict, findex, gtags)
stags = gtags
site_ids = sorted(list(gtags.keys()), key=lambda k: gtags[k])
else:
(findex, mtags) = d3bf.processtags_m(volumes, tags, dfilter)
if datatype != "raw":
(edata, site_ids,
species_ids) = d3bf.load_edata_m(data, ilevel, mn, ml, kdict, volumes,
findex, kdnames)
else:
(edata, site_ids,
species_ids) = d3bf.load_edata_m_fp(data, ilevel, mn, ml, kdict,
volumes, findex, kdnames)
stags = {}
for j in range(len(edata)):
key = ""
if order1 != "none":
key = key + mtags[order1][j]
if order2 != "none":
key = key + mtags[order2][j]
if labels != "none":
key = key + mtags[labels][j]
key = key + mtags["name"][j]
stags[key] = j
