Created
January 10, 2014 00:08
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pkm = df_tidy[df_tidy.miso_id == gene_name_to_miso_mxe['PKM'][0]] | |
fig, ax = plt.subplots(1, figsize=(8,6)) | |
sns.violinplot(pkm.value, pkm.celltype, "points", fig=fig, ax=ax, | |
color=[common.p_color, common.n_color, common.m_color, | |
common.o_color, 'white'], | |
bw=0.03, order=['iPSC', 'NPSC', 'MotorNeu', 'Outliers', 'pooled'], | |
alpha=0.75, linewidth=1) | |
sns.despine() | |
xmin, xmax, ymin, ymax = ax.axis() | |
ax.hlines((0.3, 0.7), xmin, xmax, color='k', alpha=0.8, linewidth=0.5) | |
ax.set_xlim(xmin, xmax) | |
ax.set_ylim(0, 1); |
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def celltype_to_long_name(celltype): | |
""" | |
Given a single-letter celltype string, one of 'P', 'M', or 'N', | |
(could also be lowercase) return a longer name that can be used for | |
figures, e.g. 'iPSC' instead of 'P' | |
""" | |
celltype = celltype.upper() | |
if celltype == 'M': | |
return common.m_long_name | |
elif celltype == 'N': | |
return common.n_long_name | |
elif celltype == 'P': | |
return common.p_long_name | |
elif celltype == 'O': | |
return common.o_long_name | |
elif celltype == 'POOLED': | |
return 'pooled' | |
elif celltype == 'FAILED': | |
return 'failed' | |
else: | |
raise ValueError('Invalid celltype: %s' % celltype) | |
celltype_to_ids = {'P': common.trusted_p, 'N': common.trusted_n, | |
'M':common.trusted_m, | |
'O':common.outliers, | |
'pooled':common.pooled_samples, | |
'failed':failed} | |
failed = singlecell._Common.read_single_column('/home/obot/projects/singlecell/singlecell/ignore_these_samples.txt') | |
sample_ids_to_celltype = dict((sample_id, celltype_to_long_name(celltype)) for celltype, | |
sample_ids in celltype_to_ids.iteritems() for sample_id in sample_ids) | |
gene_name = 'PKM' | |
series = mxe_summary.xs('miso_posterior_mean', axis=1, level=1).ix[gene_name_to_miso_mxe[gene_name][0]] | |
ax = sns.violinplot(series, sample_ids_to_celltype, color=[common.p_color, common.n_color, common.m_color, | |
common.o_color, 'white'], inner='points', | |
bw=0.05, order=['iPSC', 'NPSC', 'MotorNeu', 'Outliers', 'pooled'], alpha=0.75) | |
ax.set_ylim(0, 1) | |
ax.set_ylabel(gene_name) | |
sns.despine() |
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