show_2x_range=1.5,
show_legend=True,
show_count=True,
show_correlation=True,
show_plot=False,
ax=ax)
grapher.save_plot(
grapher.get_filename(
scatter_dirpath,
'two_color_kla_vs_kla_dex_group_{0}_runs_{1}.png'.
format(x, slug_label)))
grapher.show_plot()
if False:
# Gene names
print grapher.get_gene_names(refseq[(refseq['kla_1_lfc'] >= 1)],
add_quotes=True)
print grapher.get_gene_names(
refseq[(refseq['kla_1_lfc'] >= 1)
& (refseq['dex_over_kla_1_lfc'] < -.58)])
if False:
yzer = MotifAnalyzer()
motif_dirpath = yzer.get_filename(dirpath, 'motifs/size_200')
distal = data[data['distal'] == 't']
dataset = distal[(distal['kla_lfc'] >= 1)]
yzer.prep_files_for_homer(dataset,
'distal_up_in_kla_all',
motif_dirpath,
center=False,
reverse=False,
#refseq = refseq[refseq[xcolname] < max(refseq[xcolname])]
refseq_up_nond = refseq[refseq['balb_nod_notx_0h_fc'] >= 1]
refseq_down_nond = refseq[refseq['balb_nod_notx_0h_fc'] <= -1]
refseq_up_d = refseq[refseq['diabetic_balb_nod_notx_0h_fc'] >= 1]
refseq_down_d = refseq[refseq['diabetic_balb_nod_notx_0h_fc'] <= -1]
refseq_up_slowd = refseq[refseq['slow_diabetic_balb_nod_notx_0h_fc'] >= 1]
refseq_down_slowd = refseq[
refseq['slow_diabetic_balb_nod_notx_0h_fc'] <= -1]
if False:
#print set(grapher.get_gene_list(refseq_up_nond)) & set(grapher.get_gene_list(refseq_up_d))
#print set(grapher.get_gene_list(refseq_down_nond)) & set(grapher.get_gene_list(refseq_down_d))
print grapher.get_gene_names(refseq_up_nond)
if True:
# non-d
ax = grapher.scatterplot(refseq_up_nond,
'balb_notx_0h_tag_count',
'nod_notx_0h_tag_count_norm',
log=True,
color='blue',
master_dataset=refseq,
title='BALBc vs. NOD BMDC Refseq Transcripts',
show_2x_range=True,
show_legend=False,
show_count=True,
show_correlation=True,
show_plot=False)
