moving plots

Author: mikolmogorov

src/hapcorrect/main_hapcorrect.py

@@ -27,8 +27,8 @@
 from src.breakpoint.breakpoints import add_breakpoints
 from src.utils.chromosome import get_contigs_list, extract_centromere_regions, csv_df_chromosomes_sorter, df_chromosomes_sorter
 from src.cna.phaseblocks import infer_missing_phaseblocks, is_phasesets_check_simple_heuristics
-from src.hapcorrect.plots import plot_coverage_data, loh_plots_genome
-from src.hapcorrect.plot_loh import detect_loh_centromere_regions, plot_snps
+from src.plots.phasing_plots import plot_coverage_data, loh_plots_genome
+from src.plots.loh_hapcorrect import detect_loh_centromere_regions, plot_snps
 from src.hapcorrect.phase_correction import merge_contiguous_indices, find_indices_to_be_merged
 from src.coverage.smoothing import smoothing
 

src/main.py

@@ -30,11 +30,11 @@
 from src.cna.purity_ploidy import (normal_genome_proportion, weigted_means_ploidy, average_p_value_genome, dna_purity_to_cell_purity,
         move_100pct_purity_sol, find_p_values_peaks, update_segs_with_normal_optimized)
 from src.utils.statistics import weighted_means
-from src.plots import coverage_plots_chromosomes, copy_number_plots_genome_details, copy_number_plots_genome, breakpoints_segments_means, \
+from src.plots.plots_main import coverage_plots_chromosomes, copy_number_plots_genome_details, copy_number_plots_genome, breakpoints_segments_means, \
     copy_number_plots_genome_breakpoints, copy_number_plots_genome_breakpoints_subclonal, copy_number_plots_genome_subclonal, \
     genes_copy_number_plots_genome, genes_plots_genome, heatmap_copy_number_plots_genome, plot_ploidy_purity_p_values
 from src.file_tools.process_vcf import vcf_parse_to_csv_for_het_phased_snps_phasesets
-from src.snps_loh import plot_snps_frequencies_without_phasing, plot_snps_ratios_genome, snps_df_loh, variation_plots, write_loh_regions
+from src.plots.snps_loh import plot_snps_frequencies_without_phasing, plot_snps_ratios_genome, snps_df_loh, variation_plots, write_loh_regions
 from src.hapcorrect.phase_correction import generate_phasesets_bins
 from src.cna.optimization import peak_detection_optimization
 from src.file_tools.generate_vcf import read_cn_segments_process_vcf

src/plots/__init__.py

@@ -9,7 +9,7 @@
 from src.utils.chromosome import csv_df_chromosomes_sorter, df_chromosomes_sorter
 from src.cna.loh import loh_regions_phasesets_hapcorrect, detect_alter_loh_regions_hapcorrect
 from src.utils.chromosome import get_contigs_list
-from src.hapcorrect.plots import add_scatter_trace_coverage, print_chromosome_html, plots_add_markers_lines, plots_layout_settings
+from src.plots.phasing_plots import add_scatter_trace_coverage, print_chromosome_html, plots_add_markers_lines, plots_layout_settings
 
 
 def detect_loh_centromere_regions(csv_df_coverage_tumor_chrom, chrom, args, centromere_region_starts, centromere_region_ends, 

src/hapcorrect/plot_loh.py src/plots/loh_hapcorrect.pysrc/hapcorrect/plot_loh.py renamed to src/plots/loh_hapcorrect.py

@@ -11,7 +11,7 @@
 from src.file_tools.process_vcf import get_snps_frquncies, vcf_parse_to_csv_for_snps
 from src.file_tools.process_vcf_legacy import snps_mean, get_snp_segments, get_snps_frquncies_coverage, get_snps_counts, get_snps_counts_cn_regions, get_snps_frquncies_genome
 from src.utils.chromosome import get_contigs_list, csv_df_chromosomes_sorter
-from src.plots import add_scatter_trace_coverage, print_chromosome_html, plots_add_markers_lines, plots_layout_settings,\
+from src.plots.plots_main import add_scatter_trace_coverage, print_chromosome_html, plots_add_markers_lines, plots_layout_settings,\
 whole_genome_combined_df, copy_number_plots_per_chromosome, print_genome_pdf, add_annotation
 from src.cna.loh import detect_alter_loh_regions, detect_alter_loh_regions
 from src.output.writers import write_header_comments