makeTexFile: makeTexFile.R

Description Usage Arguments Value Examples

Description

The makeTexFile function generates the LaTeX file that generates the visual output of the scoring between the given alignments.

Details.

Usage

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makeTexFile(reference, compare, SP = TRUE, CS = TRUE, filename,
  filepaths, score, scorePaths)

Arguments

reference

A directory path to the reference alignment the user would like to use

compare

A directory path to the alignment being compared to the reference alignment

SP

A boolean value left TRUE if the user would like to generate the sum of pairs in their output

CS

A boolean value left TRUE if the user would like to generate the total column score in their output

filename

The preferred name of the output file

filepaths

The paths to the copied and modified alignment files

score

The pairwise alignment score object generated by AlignStat of the two alignments provided by the user

scorePaths

The path to the data containing columnwise scores for the sum of pairs score and total column score

Value

The filepath to the generated Tex file is returned

Examples

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reference <- "data/BB11017ClustalW.fasta"
test <- "data/BB11017Muscle.fasta"
fileName <- "sampleTest2"

score <- getScore(reference, test)
filePaths <- modifyAlns(reference, test, fileName)
scorePaths <- makeScoreFile(reference, compare, SP, CS, fileName, score)

texpath <- makeTexFile(reference, test, fileName, filepaths, score,
                      scorePaths)
texpath

judyheewonlee/ScoreVisualizer documentation built on May 31, 2019, 5:20 p.m.