# Remove low tag counts
#refseq = refseq[refseq['transcript_score'] >= 4]
sets.append(refseq)
if True:
genes = ['Coro1a', 'Vcl', 'Tlr2', 'Clec4e', 'Cxcl2']
vals = []
labels = []
for gene in genes:
vals.append(sets[0][sets[0]['gene_names'] == gene]
['balb_nod_notx_1h_fc'].values[0])
vals.append(sets[1][sets[1]['gene_names'] == '{' + gene +
'}']['balb_nod_notx_0h_fc'].values[0])
labels.append('ThioMac\n' + gene)
labels.append('BMDC\n' + gene)
# Convert to FC from log
vals = [2**val for val in vals]
yzer.bargraph_for_transcripts(
vals,
None,
None,
bar_names=labels,
title='NOD vs. BALBc NOTX GRO-seq: ThioMac and BMDC',
ylabel='Fold Change in NOD vs. BALBc',
show_plot=True,
save_dir=img_dirpath)
#'srf_targets': ['Srf','Cnn2','Lima1','Coro1a','Vcl','Acta2','Actb','Dhcr24','Actg2','Actc1','Lcp1','Jup','Tpm4','Tnni2','Zyx','Tubb3','Pfn1','Gas7','Arpc4','Pstpip1','Bsn','Flna','Actn1'],
#'inflammatory_genes': ['Cxcl1','Cxcl2','Il6','Ptgs2','Tnfsf9','Vegfa','Tnf', 'Siglec1','Mmp9', 'Il10','Il1b','Cxcl10','Tlr4','Il12b',]
}
'''
'clec4e_tlr2': ['Clec4e','Tlr2',],
,
'''
for i, genes in gene_groups.items():
for gene in genes[:]:
if not gene in refseq['gene_names'].values:
print gene
genes.remove(gene)
indices = [refseq[refseq['gene_names'] == gene].index[0] for gene in genes]
for txt in ('notx','kla'):
sorted_by_count = refseq.fillna(0).sort_index(axis=0, by='balb_{0}_1h_reads_per_base'.format(txt)).index.copy()
sort_indexes = list(enumerate(sorted_by_count))
sort_indexes.sort(key=lambda x: x[1])
refseq['rank'] = zip(*sort_indexes)[0]
yzer.bargraph_for_transcripts(refseq, indices, ['balb_nod_{0}_1h_fc'.format(txt)],
bar_names=genes,
title='NOD vs. BALBc {0} 1h GRO-seq'.format(txt=='kla' and txt.upper() or txt.capitalize()),
ylabel='Fold Change in NOD vs. BALBc',
rank_label='Rank of read per base pair value\nin BALBc {0} 1h, ascending'.format(
txt=='kla' and txt.upper() or txt.capitalize()),
show_plot=False)
yzer.save_plot(yzer.get_filename(img_dirpath, 'balbc_nod_{0}_{1}_fold_change_bargraph.png'.format(txt,i)))
#yzer.show_plot()
