| Title: | Visualizing Sequence Alignment by Generating Publication-Ready Plots |
| Version: | 0.1 |
| Author: | Mohamed Soudy [aut, cre] |
| Maintainer: | Mohamed Soudy <MohmedSoudy2009@gmail.com> |
| Description: | Providing publication-ready graphs for Multiple sequence alignment. Moreover, it provides a unique solution for visualizing the multiple sequence alignment without the need to do the alignment in each run which is a big limitation in other available packages. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.2 |
| Imports: | ggplot2, ggmsa, reshape2 |
| NeedsCompilation: | no |
| Packaged: | 2023-06-13 18:43:32 UTC; Soudy |
| Repository: | CRAN |
| Date/Publication: | 2023-06-14 16:22:05 UTC |
Convert string to a character vector
Description
convert string that can be DNA or protein sequence to a character vector
Usage
Seqtochar(x)
Arguments
x |
a sequence of DNA or Protein |
Value
this function is mainly used by ggaligner function to convert the input sequence to character vector
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com
Examples
Seqtochar("ATGACATAAT")
Visualize the alignment object from msa package
Description
Generating a plot for msa object of DNA or Protein sequence
Usage
ggaligner(alignment,start=1,end=10,color="Clustal",font="helvetical",label_font = 12)
Arguments
alignment |
alignment object returned from msa package |
start |
start position of the desired alignment region |
end |
end position of the desired alignment region |
color |
color scheme to use ex: Clustal, Chemistry_AA, Shapely_AA |
font |
font family to use ex: helvetical, TimesNewRoman |
label_font |
font size of sequence names |
Value
An enhanced plot for the alignment using ggplot2 and ggmsa packages
Author(s)
Mohamed Soudy Mohmedsoudy2009@gmail.com