#' <% visualizations.ShotGun.print_qc_intro_caption(len(dna_samples), dna_columns[2:]) %> #' ## DNA Samples Quality Control #' ### DNA Samples Tables of Filtered Reads #+ echo=False # create a table of the paired counts document.write_table(["# Sample"] + dna_columns, dna_samples, dna_data, files.ShotGunVis.path("qc_counts", document.data_folder)) table_message = visualizations.show_table_max_rows( document, dna_data, dna_samples, dna_columns, "DNA reads", files.ShotGunVis.path("qc_counts"), format_data_comma=True) #' <%= table_message %> #+ echo=False # compute and plot the microbial reads ratios # compute ratios for each database used for qc dna_microbial_reads, dna_microbial_labels = utilities.microbial_read_proportion_multiple_databases( dna_data, dna_columns) # create a table of the microbial reads document.write_table(["# Sample"] + dna_microbial_labels, dna_samples, dna_microbial_reads,
all_taxa_counts = [[ a, b, c, d ] for a, b, c, d in zip(species_counts, species_counts_after_filter, genera_counts, genera_counts_after_filter)] # create a table of the data in the output folder taxa_counts_column_names = [ "# Sample", "Species", "Species filtered", "Genera", "Genera filtered" ] document.write_table( taxa_counts_column_names, samples, all_taxa_counts, files.ShotGunVis.path("taxa_counts", document.data_folder)) # show the table, reducing the rows if there are lots of samples table_message = visualizations.show_table_max_rows( document, all_taxa_counts, samples, taxa_counts_column_names[1:], "Total taxa per sample", files.ShotGunVis.path("taxa_counts")) #' <%= table_message %> #' ## Ordination #' ### Species #+ echo=False # get the top species by average abundance top_taxonomy, top_data = utilities.top_rows(species_taxonomy, species_data, max_sets_heatmap, function="average")
#' <%= visualizations.ShotGun.format_caption("pathway_abundance_heatmap",norm="z-score") %> #' <% if pdf_format: print("\clearpage") %> #+ echo=False # write a table of the pathways average and variance pathway_file_name = "top_average_pathways_names.tsv" average_abundance_variance = visualizations.write_pathway_average_variance_table( document, pathway_file_name, dna_top_average_data, top_names_and_descriptions) table_message = visualizations.show_table_max_rows( document, average_abundance_variance, top_names_and_descriptions, [" Average ", " Variance "], "Top " + str(max_sets) + " pathways by average abundance", pathway_file_name, font=7) #' <%= table_message %> #' <% visualizations.print_pathways_urls(dna_top_average_pathways,top_names_and_descriptions,3) %> #+ echo=False # check for then rna/dna norm files show_norm_ratio = False if vars["genefamilies_norm_ratio"] and vars["ecs_norm_ratio"] and vars[ "paths_norm_ratio"]: show_norm_ratio = True
#+ echo=False #' ## DNA Samples Quality Control #' ### DNA Samples Tables of Filtered Reads #+ echo=False document.write_table(["# Sample"] + dna_paired_columns, dna_samples, dna_paired_data, files.ShotGunVis.path("qc_counts_paired", document.data_folder)) table_message = visualizations.show_table_max_rows( document, dna_paired_data, dna_samples, dna_paired_columns, "DNA Paired end reads", files.ShotGunVis.path("qc_counts_paired"), format_data_comma=True) #' <%= table_message %> #+ echo=False document.write_table(["# Sample"] + dna_orphan_columns, dna_samples, dna_orphan_data, files.ShotGunVis.path("qc_counts_orphan", document.data_folder)) table_message = visualizations.show_table_max_rows( document, dna_orphan_data,