MultiFunctionTaxaContributionPlots: A function to plot different versions of the FishTaco plot...

In borenstein-lab/fishtaco-plot: Functions to Produce the FishTaco Plots

Description

A function to plot different versions of the FishTaco plot for multiple functions

Usage

MultiFunctionTaxaContributionPlots(input_dir = NULL, input_prefix = NULL,
  input_suffix = ".tab", input_score = "wilcoxon",
  input_contribution = "taxa_contributions",
  input_original = "original_value", input_permutation = "multi_taxa",
  input_predicted_da = "predicted_DA_value",
  input_predicted_function = "predicted_function_abundance",
  input_predicted_residual = "residual_function_abundance",
  input_predicted_abundance_agreement = "predicted_function_agreement",
  input_inference_copy_number = "taxa_learned_copy_num",
  input_taxa_da = "DA_taxa", input_function_abundance = NULL,
  input_function_meta = NULL, input_taxa_taxonomy = NULL,
  input_taxa_vs_function = NULL, input_function_counts = NULL,
  input_function_stats = NULL, input_function_filter_list = NULL,
  input_function_filter_file = NULL, plot_type = "bars",
  sort_by = "predicted_da", min_contribution = 0,
  min_cont_as_separate = 0.025, min_function_counts = 0,
  min_shift_explained = 0, max_function_to_show = NULL,
  show_only_diff_abun_taxa = FALSE, show_only_pos = FALSE,
  show_only_neg = FALSE, show_only_taxa_with_function = FALSE,
  show_only_enriched_taxa = FALSE, show_only_enriched_functions = FALSE,
  show_only_depleted_taxa = FALSE, show_only_depleted_functions = FALSE,
  scale_pos_by_original_pos_sum = FALSE,
  scale_neg_by_original_neg_sum = FALSE, add_facet_labels = FALSE,
  add_names_in_bars = FALSE, add_taxa_da = FALSE,
  add_case_control_line = FALSE, add_predicted_da_markers = TRUE,
  add_original_da_markers = FALSE, add_phyla_names_to_species_label = FALSE,
  color_small_cont_by_phyla = FALSE, input_bar_width = NULL,
  verbose = FALSE, flip_coord = TRUE, split_function_names_2_lines = TRUE,
  separate_enriched_depleted_taxa = TRUE, use_facets_for_separation = FALSE,
  flip_case_control = FALSE)

Arguments

input_dir	The directory where all the FiShTaCo input files can be found (default: NULL).
input_prefix	The prefix for all input files (e.g., pathway_with_t2f, default: NULL).
input_suffix	The suffix for all input files (default: ".tab").
input_score	The calculated shift scoring metric (default: wilcoxon).
input_contribution	The taxon-level contribution profile (default: "taxa_contributions").
input_original	The original (metagenome-based) calculated shift (default: "original_value").
input_permutation	The permutation type used (default: "multi_taxa").
input_predicted_da	The predicted (taxa-based) shift score (default: "predicted_DA_value").
input_predicted_function	The predicted (taxa-based) functional abundance (default: "predicted_function_abundance").
input_predicted_residual	The residual functional abundance (default: "residual_function_abundance").
input_predicted_abundance_agreement	The agreement between the taxa- and metagenome based functional abundance (default: "predicted_function_agreement").
input_inference_copy_number	The inferred copy number for each function (default: "taxa_learned_copy_num").
input_taxa_da	The calculated taxonomic composition shift score (default: "DA_taxa").
input_function_abundance	The metagenome-based functional abundance (default: NULL).
input_function_meta	Metadata on the given functions (default: NULL).
input_taxa_taxonomy	Phylogenetic assignment for each taxon (default: NULL).
input_taxa_vs_function	The genomic content of each taxon (default: NULL).
input_function_counts	The median count of functions across samples (default: NULL).
input_function_stats	Statistics about each function across the taxa (default: NULL).
input_function_filter_list	A list of specific functions to plot (default: NULL).
input_function_filter_file	A file containing a list of specific functions to plot (default: NULL).
plot_type	The type of plot to be plotted (default: "bars").
sort_by	How to sort the functions in the plot (default: "predicted_da").
min_contribution	Minimum taxon contribution to plot (default: 0).
min_cont_as_separate	Minimum contribution to plot as separate species (default: 0.2).
max_function_to_show	Maximum number of functions to show (default: NULL).
show_only_diff_abun_taxa	Show only taxa that shift in abundance (default: FALSE).
show_only_pos	Show only taxa that contribute positively (drive) to the shift (default: FALSE).
show_only_neg	Show only taxa that contribute negatively (attenuate) to the shift (default: FALSE).
show_only_taxa_with_function	Show only taxa that have the function in their genome (default: FALSE).
show_only_enriched_taxa	Show only taxa that are case-associated (default: FALSE).
show_only_enriched_functions	Show only functions that are case-enriched (default: FALSE).
show_only_depleted_taxa	Show only taxa that are control-associated (default: FALSE).
show_only_depleted_functions	Show only functions that are control-enriched (default: FALSE).
scale_pos_by_original_pos_sum	Scale driving contribution by their sum (default: FALSE)
scale_neg_by_original_neg_sum	Scale attenuating contribution by their sum (default: FALSE)
add_facet_labels	Add labels to each function (default: FALSE).
add_names_in_bars	Add taxa names in the bars (default: FALSE).
add_taxa_da	Add a top bar of taxonomic shifts (default: FALSE).
add_case_control_line	Add a line separating case- and control-enriched functions (default: FALSE).
add_predicted_da_markers	Add diamond markers for the taxa-based shift score (default: TRUE).
add_original_da_markers	Add diamond markers for the metagenome-based shift score (default: FALSE).
input_bar_width	Defines the width of the bars (default: NULL).
verbose	Run with verbose (default: FALSE).
flip_coord	Flip axis to show horizontal bars (default: TRUE).
split_function_names_2_lines	Splits function names into 2 lies (default: TRUE).
separate_enriched_depleted_taxa	Separate case- and control-associated taxa (default: TRUE).
use_facets_for_separation	Use facets for separation of functions (default: FALSE).
flip_case_control	Switch between cases and controls (default: FALSE).

Value

a handle to the resulting plot.

borenstein-lab/fishtaco-plot documentation built on July 7, 2021, 4:18 a.m.