Commit f17dcbd8 authored by Beatrice Tan's avatar Beatrice Tan

Updated reports.

parent b6e501b7
......@@ -20,11 +20,11 @@ def make_report(size_gistic, size_rubic_gains, size_rubic_losses, census_genes,
for tool in 'GISTIC', 'RUBIC':
size_file = (size_rubic_gains[i], size_rubic_losses[i]) if tool == 'RUBIC' else size_gistic[i]
parsed_results = parse_regions(size_file, known_genes, census_genes, tool)
if tool not in all_results.keys():
all_results[tool] = {}
all_results[tool][size] = [parsed_results]
else:
all_results[tool][size] = all_results[tool][size] + [parsed_results]
#if tool not in all_results.keys():
# all_results[tool] = {}
# all_results[tool][size] = [parsed_results]
#else:
# all_results[tool][size] = all_results[tool][size] + [parsed_results]
stats_results = get_stats(parsed_results, size)
for stat_list in stats_results[0], stats_results[1]:
converted_stats = [tool] + stat_list[0:2]
......@@ -33,7 +33,7 @@ def make_report(size_gistic, size_rubic_gains, size_rubic_losses, census_genes,
for stat in stat_list[5:]:
converted_stats.append(float(stat.split(" (")[0]))
list_stats.append(converted_stats)
overlap_genes(all_results, report_file)
#overlap_genes(all_results, report_file)
make_plots(list_stats, reps, sizes, plot_dir)
def overlap_genes(all_results, report_file):
......@@ -60,7 +60,7 @@ def plot_size_differences(df_stats, value_y_axis, list_sizes, nr_reps, plot_dir)
"""Plot the differences between analyses using different sample sizes."""
sns.set_style("whitegrid")
g = sns.factorplot(x="Sample size", y=value_y_axis, col="Type", hue="Tool", data=df_stats, kind="box",
size=5, aspect=1, palette=sns.cubehelix_palette(8, start=.5, rot=-.75, dark=.2))
size=5, aspect=1, palette=["#5975A4","#5F9E6E"])
g.set_axis_labels("Sample size", value_y_axis).set_titles("{col_name}").despine(bottom=True)
#add_significance(g, df_stats, list_sizes, value_y_axis)
png_file = os.path.join(plot_dir, value_y_axis.replace(" ", "_") + ".png")
......
......@@ -24,11 +24,11 @@ def make_report(gistic_results, rubic_gain_results, rubic_loss_results,
parsed.append(parsed_results)
stats.append(get_stats(parsed_results, tool))
stats.append(parse_bed_overlap(bed_overlap, known_genes, census_genes))
table_all_regions(parsed, file_regions) #make table with all regions
make_tool_report(file_tools, stats) #make tool report
table_all_regions(parsed, file_regions) #make table with all regions
make_tool_report(file_tools, stats) #make tool report
all_genes = make_gene_files(parsed, file_genes_GISTIC, file_genes_RUBIC, file_genes_both, known_genes, file_venn) #make gene files and venn overlap plot
plot_histogram_sizes(parsed, file_swarmplot) #plot histogram with the sizes of the regions
make_bed_known_regions(known_genes, biomart_file, bed_known_genes) #Make bed file with the locations of known genes.
plot_histogram_sizes(parsed, file_swarmplot) #plot histogram with the sizes of the regions
make_bed_known_regions(known_genes, biomart_file, bed_known_genes) #Make bed file with the locations of known genes.
def make_tool_report(file_tools, stats_tools):
"""Make a report of the results from GISTIC and RUBIC."""
......@@ -86,6 +86,8 @@ def make_gene_file_overlap(gene_lists, out_both):
def venn3_overlap(gene_lists, known_genes, out_venn):
known = parse_gene_file(known_genes, np.inf)
plt.subplots(figsize=(7, 7))
overlap_tools = set(gene_lists[0]).intersection(set(gene_lists[1]))
print(overlap_tools.intersection(set(known)))
venn_sets = [set(gene_lists[0]), set(gene_lists[1]), set(known)]
c = venn3(venn_sets, ('GISTIC2', 'RUBIC', ' Known genes'))
c.get_patch_by_id('100').set_color('#5975A4'), c.get_patch_by_id('010').set_color('#5F9E6E')
......
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