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)