def plot_venn_de_directions(
logfc,
set_colours_dict,
ax=None,
set_labels=('Hypo', 'Hyper'),
fontsize=16
):
if ax is None:
fig = plt.figure(figsize=(5., 3.3))
ax = fig.add_subplot(111)
vv, vs, vc = venn.venn_diagram(
*[logfc[k].index[logfc[k]['consistent'].astype(bool)] for k in set_labels],
set_labels=set_labels,
set_colors=[set_colours_dict[t] for t in set_labels],
ax=ax
)
ax.figure.tight_layout()
# modify labels based on direction
this_members = collections.OrderedDict()
for k in set_labels:
this_res = logfc[k]
this_ix = this_res['consistent'].astype(bool)
this_res = np.sign(this_res.loc[this_ix].astype(float).mean(axis=1))
this_members["%s up" % k] = this_res.index[this_res > 0].difference(vs['11'])
this_members["%s down" % k] = this_res.index[this_res < 0].difference(vs['11'])
# get the corresponding label
lbl = vv.get_label_by_id(setops.specific_sets(set_labels)[k])
## FIXME: font family seems to change from old text to new - related to LaTeX rendering?
lbl.set_text(
lbl.get_text()
+ '\n'
+ r'$%d\uparrow$' % len(this_members["%s up" % k])
+ '\n'
+ r'$%d\downarrow$' % len(this_members["%s down" % k]),
)
plt.setp(common.get_children_recursive(ax, type_filt=plt.Text), fontsize=fontsize)
return ax
# DE
pids = consts.PIDS
outdir = output.unique_output_dir()
# load previously generated DE results
fn = os.path.join(HGIC_LOCAL_DIR, 'current', 'core_pipeline', 'rnaseq',
'full_de_syngeneic_only.xlsx')
de_res = pd.read_excel(fn, header=0, index_col=0)
all_ens = de_res.index[(de_res[pids] == 'Y').any(axis=1)]
de_per_pat = {pid: de_res.index[de_res[pid] == 'Y'] for pid in pids}
n_tot = {pid: de_per_pat[pid].size for pid in pids}
vs, vc = setops.venn_from_arrays(*[de_per_pat[pid] for pid in pids])
pp = setops.specific_sets(pids)
n_ps = {pid: vc[pp[pid]] for pid in pids}
# perms
n_all = len(all_ens)
n_spec = run_patient_specific_permutations(n_tot, n_all, n_perm=n_perm)
fig, axs = plot_perms_kde_vs_obs(
n_spec, n_ps, xlabel='Number of patient-specific DE genes', order=pids)
fig.savefig(os.path.join(outdir, "patient_specific_de.png"), dpi=200)
fig.savefig(os.path.join(outdir, "patient_specific_de.tiff"), dpi=200)
fig.savefig(os.path.join(outdir, "patient_specific_de.pdf"))
fn = os.path.join(HGIC_LOCAL_DIR, 'current', 'core_pipeline',
'methylation', 'full_dmr_syngeneic_only.xlsx')
dm_res = pd.read_excel(fn)
for t in joint_de_dmr_s1.values()]))
dgi_all = druggable_genome.dgidb_lookup_drug_gene_interactions(all_genes)
# manually resolve a few known ambiguities
ambig = {'ELTD1': 'ADGRL4', 'ODZ3': 'TENM3'}
for k, v in ambig.items():
x = [t for t in dgi_all['ambiguous'][k] if t['geneName'] == v][0]
dgi_all['interactions'][k] = x['interactions']
de_dmr_by_member = [joint_de_dmr_s1[pid].index for pid in pids]
venn_set, venn_ct = setops.venn_from_arrays(*de_dmr_by_member)
# define short and long list
# long list
ss = setops.specific_sets(pids)
ps_de_dm_long = collections.OrderedDict([(pid, venn_set[ss[pid]])
for pid in pids])
ps_de_dm_long_list = setops.reduce_union(*ps_de_dm_long.values())
# short list
vs_dm, vc_dm = setops.venn_from_arrays(
*[dmr_res_s1[pid].results_significant.keys() for pid in pids])
vs_de, vc_de = setops.venn_from_arrays(
*[de_res_s1[pid]['Gene Symbol'].dropna() for pid in pids])
ps_dm = {pid: vs_dm[v] for pid, v in ss.items()}
ps_dm_genes = {}
for pid, cids in ps_dm.items():
ps_dm_genes[pid] = sorted(