makeAlignmentPDF: Function to generate PDF files holding an alignment using the...

In Fraternalilab/BrepPhylo: BrepPhylo: R package for phylogenetic analysis of B cell repertoire

Function to generate PDF files holding an alignment using the function msaPrettyPrint_extended and LaTeX.

Description

Function to generate PDF files holding an alignment using the function msaPrettyPrint_extended and LaTeX.

Usage

makeAlignmentPDF(clone, alignment, cloneIdColumn, outputFolder, colours)

Arguments

clone	Clone dataframe.
alignment	Alignment for the clone (including the germline sequence at the first position).
cloneIdColumn	Name of the column holding the clone IDs.
outputFolder	Path to the output folder.
colours	A named vector of HTML colours for the sequences (including the '#' sign).

Examples

## Not run: makeAlignmentPDF <- function( clone = clone,
                              alignment = alignment,
                              cloneIdColumn = "Unique_CloneID",
                              outputFolder = "~/Desktop",
                              colours = colours )
## End(Not run)

Fraternalilab/BrepPhylo documentation built on Jan. 3, 2025, 10:03 a.m.