plot_cc: Plot peptide-to-protein mapping graph

In laurafancello/CCs4prot: Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Plot peptide-to-protein mapping graph

Description

Plot a bipartite subgraph representing the connected component to which the user-selected protein belongs. Peptide-to-protein mappings of that protein and of all other proteins belonging to the same CC are represented. The function takes in input a single Ensembl protein identifier (i.e. ENSPXXX for human, ENSMUSPXXX for mouse), it identifies the connected component it belongs to and plots all peptide-to-protein mappings of that connected component.

Usage

plot_cc(prot, cc.proteins, cc.subincM, tagProt, tagContam, incM)

Arguments

prot	a character vector containing a single Ensembl identifier (i.e. ENSPXXXXXXXXXXX for human, ENSMUSPXXXXXXXXXXX for mouse) of the protein of interest.
cc.proteins	a list of vectors (one for each connected component) containing protein members of each connected component.
cc.subincM	a list of matrices or vectors (one for each connected component) representing the incidence matrix of peptide-to-protein mappings for each connected component; matrices are used if multiple peptides identify protein members of that connected component, vectors if only a single peptide.
tagProt	a character vector reporting the prefix of protein identifiers (for non contaminant proteins)
tagContam	a character vector reporting the tag which identifies contaminant proteins
incM	a logical matrix containing the incidence matrix with its column and row names (respectively, protein and peptide identifiers) names and 0 or 1 values indicating whether or not the peptide maps on the corresponding protein.

Value

a list of four elements: i. CC identifier; ii. protein members of the CC; iii. peptide members of the CC; iv. bipartite subgraph representing peptide-to-protein mapping of that CC (if multi-protein CC)

Author(s)

Laura Fancello

Examples

library(igraph)
# Read the tab-delimited file containing he proteome incidence matrix
incM_filename <- system.file( "extdata"
                             , "incM_example"
                             , package = "net4pg"
                             , mustWork = TRUE)
rownames_filename <- system.file( "extdata"
                                  , "peptideIDs_incM_example"
                                  , package = "net4pg"
                                  , mustWork = TRUE)
colnames_filename <- system.file( "extdata"
                                 , "proteinIDs_incM_example"
                                 , package = "net4pg"
                                 , mustWork = TRUE)
incM <- read_inc_matrix(incM_filename = incM_filename
                 , colnames_filename = colnames_filename
                 , rownames_filename = rownames_filename)
# Only retain proteins with at least one shared peptide and all peptides
# mapping on such proteins.
incM_reduced <- reduce_inc_matrix(incM)
# Generate adjacency matrix describing protein-to-protein mappings
adjM <- get_adj_matrix(incM_reduced)
# Generate graph of protein-to-protein connections and calculate its
# connected components
multProteinCC <- get_cc(adjM)
# For each connected component, extract peptides mapping on its protein
# members and the subset of the incidence matrix describing
# peptide-to-protein mappings
cc.peptides.incM <- cc_composition(cc.proteins = multProteinCC$cc
                                   , incM = incM)
# Plot bipartite graph representing peptide-to-protein mappings for the
# connected component of the protein of interest (in this toy example protein
# "ENSP261"; note that identifiers are not authentic but made up for the
# example)
subgraphCC <- plot_cc(prot="ENSP261"
        , cc.proteins=multProteinCC$ccs
        , cc.subincM=cc.peptides.incM$cc.subincM
        , tagProt = "ENSP"
        , tagContam="Contam"
        , incM=incM)
plot.igraph(subgraphCC$g
      , layout = layout_as_bipartite
      , edge.width = 1
      , edge.arrow.width = 0.3
      , vertex.size = 10
      , edge.arrow.size = 0.5
      , vertex.size2 = 3
      , vertex.label.cex = 0.8
      , asp = 0.35
      , margin = -0.1) +
title(paste0("Protein ENSP261 in CC #", subgraphCC$cc_id), line = -1)

laurafancello/CCs4prot documentation built on July 1, 2022, 1:34 p.m.