SingleFunctionTaxaContributionPlots: Plots one of the following plots for a single function: -...

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

Description

Plots one of the following plots for a single function: - Steps plot with mean and std contributions for all taxa - Ring plot where the contributions are shown as a ring - Bar plot where the contributions are shown as a bar

Usage

SingleFunctionTaxaContributionPlots(input_dir = NULL, input_prefix = NULL,
  input_suffix = ".tab", input_score = "wilcoxon",
  input_matrix_mean = "mean_stat", input_matrix_std = "std_stat",
  input_permutation = "multi_taxa", input_original = "original_value",
  input_function = NULL, min_contribution = 0, input_function_meta = NULL,
  input_taxa_taxonomy = NULL, plot_type = "steps",
  flip_case_control = FALSE, class_label_1 = NULL, class_label_2 = NULL,
  add_phyla_names_to_species_label = 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 score for all input files (default: wilcoxon).
input_matrix_mean	The mean contribution stat name (default: "mean_stat").
input_matrix_std	The contribution std stat name (default: "std_stat").
input_permutation	The permutation type used for all input files (default: "multi_taxa").
input_original	The original shift stat name (default: "original_value").
input_function	The function to plot (default: NULL).
min_contribution	The minimum taxon contribution to include in plot (default: 0).
input_function_meta	Metadata file for the functions to include (default: NULL).
input_taxa_taxonomy	Taxonomy file for the given taxa (default: NULL).
plot_type	defines the type of plot to be plotted (default: "steps").
flip_case_control	flip the case and control contribution (default: FALSE).
class_label_1	label for the the controls (default: NULL).
class_label_2	label for the the cases (default: NULL).
add_phyla_names_to_species_label	indicating whether to add the phylum to each species (default: FALSE).

Value

a handle to the resulting plot.

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