makeTexFile: makeTexFile.R

In judyheewonlee/ScoreVisualizer: Score Visualizer

Description

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

Details.

Usage

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

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.