plot_structure_on_protein: Plot structure entropy on protein background

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function enables to visually asses the stucture(s) entropy in comparison with protein's entropy

Usage

plot_structure_on_protein(protein_entropy, structure_profiles,
  pdb_name = NULL, colors = NULL, structure_names = NULL,
  legend_pos = NULL)

Arguments

protein_entropy	A list of entropy values for protein of interest. Output of get_prot_entropy function
structure_profiles	Output of prepare_structure_profile function
pdb_name	(optional) A string with protein's name e.g. PDB ID.
colors	(optional) A vector of strings with colors to be used to plot the stucture markers of length equal to number of structures in structure profiles, default: rainbow()
structure_names	(optional) A vector of strings to be displayed as names in the legend, default: "stru <no>"
legend_pos	(optional) A string witch legend position - one of following: "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Default: "bottomleft"

Details

For each entropy score from structure_profiles (these must correspond to prot_entropy) this function plots separate plots. Each plot presents entropy score for whole protein each structure is marked as one of 21 symbols available in generic plot function.

Value

This function produces plot

Examples

data("alignment")
data("structure")
indices=get_structures_idx(structure)
protein_index = indices$proteinIndices
structure_index = indices$structureIndices
entropy_scores_list=list(Schneider_entropy = schneider_conservativity(alignment),
                                   Escore_entropy = Escore_conservativity(alignment))
structure_entropy=get_structures_entropy(structure_index, entropy_scores_list)
structure_profile = prepare_structure_profile(structure, structure_entropy)
prot_entropy=get_prot_entropy(protein_index, entropy_scores_list)

plot_structure_on_protein(prot_entropy, structure_profile)

michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.