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Commit ac9207e2 authored by Argyris Z's avatar Argyris Z
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Various comparisons used in the text

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import common.lin as lin
import grates as grs
import patternTransitions as p
import growth_control as gc
import numpy as np
from scipy.stats import ttest_ind
def gratio(xs, xs1):
if not xs or not xs1:
return 0.0
m1 = np.median(xs)
m2 = np.median(xs1)
return (m1 - m2) / (m1 + m2)
#load FM1 at specified timepoints
tss, linss = lin.mkSeries1(d="../data/FM1/tv/",
dExprs="../data/geneExpression/",
linDataLoc="../data/FM1/tracking_data/",
ft=lambda t: t in {10, 40, 96, 120, 132})
lin.filterL1_st(tss)
grates = grs.grates_avg_cons(tss, linss)
grates_gene = p.getGAnisosPerGene(tss, grates)
grates_st = gc.get_grs_state()
rgd_g = {}
for g in set(grates_gene.keys()).difference(set(['AHP6'])):
grs1 = grates_gene['AHP6']
grs2 = grates_gene[g]
_, pval = ttest_ind(grs1, grs2)
rgd_g[g] = (gratio(grs1, grs2),
pval)
rgd_g_ = {}
for g in set(grates_gene.keys()).difference(set(['CUC1_2_3'])):
grs1 = grates_gene['CUC1_2_3']
grs2 = grates_gene[g]
_, pval = ttest_ind(grs1, grs2)
rgd_g_[g] = (gratio(grs1, grs2),
pval)
rgd_st26 = {}
for g in set(grates_st.keys()).difference(set([26, 27])):
grs1 = grates_st[26] + grates_st[27]
grs2 = grates_st[g]
_, pval = ttest_ind(grs1, grs2)
rgd_st26[g] = (gratio(grs1, grs2),
pval)
rgd_st16 = {}
for g in set(grates_st.keys()).difference(set([16, 17])):
grs1 = grates_st[16] + grates_st[17]
grs2 = grates_st[g]
_, pval = ttest_ind(grs1, grs2)
rgd_st16[g] = (gratio(grs1, grs2),
pval)
t=132
ts = tss[t]
g = gc.GPairRegions(t, ts, 'ETTIN', 'STM')
g1 = gc.GPairRegions(t, ts, 'AP1', 'LFY')
g.plot_distr()
g1.plot_distr()
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