Generate pdf multiple sequence alignment logos for identified aligning groups.

groupMSA(
  groups,
  mpath = "intermediate_files/msa/",
  min.groupsize = 2,
  min.consensus.pos = 1,
  consensus.type = "Biostrings",
  consensus.thresh = c(100, 49),
  peptide.nchar = 50,
  msa.width = "dynamic",
  pdflatex = TRUE,
  pdftk = TRUE,
  pdfuniter = FALSE,
  make.png = FALSE
)

Arguments

groups

Table of final peptides and pre-calculated groupings.

mpath

Directory to write sequence alignment files.

min.groupsize

Minimum number of peptides per group to require in order to print a group.

min.consensus.pos

Minimum number of amino acid consensus positions required in order to print a group.

consensus.type

"upperlower" or "Biostrings" type of msa consensus sequence to output

consensus.thresh

Two decreasing numeric values of upper and lower thresholds for sequence consensus. ONly valid for consensus.type == "upperlower".

peptide.nchar

Maximum of character from peptide name to use in msa output. Default 50. Starts from left.

msa.width

Controls whether or not MSA images have fixed or dynamic width. By default, msa.width is set to "dynamic", which causes the document dimentions of the resultant image to be calculated based on the lentht of the peptide name and the number of amino acids in the sequence alignment. If msa.width is instead set to a numeric, then an MSA will be printed with a fixed with that number of inches. With 50-character peptide.nchar and a maximum expected sequence alignment of 45 positions, an msa.width of 12 is more than sufficient.

pdflatex

Logical whether or not to produce PDF LaTeX figures using pdflatex

pdftk

Logical whether or not to use staplr and pdftk to merge individual msa pdfs.

pdfuniter

Logical whether or not to merge msa pdfs using staplr and pdfuniter

make.png

Locial whether or not to convert PDF output to PNG.